CA2235223A1 - Rationally designed polysaccharide lyases derived from heparinase i - Google Patents

Abstract

Modified heparinases having altered binding specificity and activity are provided. Isolated nucleic acids encoding the same as well as vectors and host cells are provided. Methods for using the modified heparinases are also provided.

Description

CA 0223~223 1998-04-29 W O 97/16556 PCTrUS96117310 RATIONALLY DESIGNED POI,~SACCHARIDE LYAS~,~
D~RTVED FROM ~F,PARINASE I

Goverr rlent Support The present invention was supported in part by a grant from the United States 10 National Institutes of Health (GM 25810). The U.S. government retains certain rights in the invention.

Field of the Invention The present invention relates to polysaccharide lyases and the rational design of the 15 same. In particular, the present invention relates to new polysaccharide lyases rationally designed and based upon the heparinase I of Flavobacterinm he~h p~a~ roupd of the Invention The polysaccharidc~ heparin and heparin sulfate are characterized by a disaccharide 20 repeating unit of uronic acid and hexosarnine, where the uronic acid is either L-iduronic acid or D-glucuronic acid and the glucosamine is linked to the uronic acid by a 1 ~4 linkage (Jackson et al., 1991). Heparin-like molecules are complex due to the high degree and varying patterns of sulfation on both the uronic acid and the hexosamine residll~s It is believed that it is the sulfation which is responsible for the numerous dirr~l~,ll functional 25 roles of these carbohydrates. Our understan~1inp~ of heparin's functional role is severely limited by our poor knowledge of the heparin sequence.
Heparina~es have proved to be useful tools in heparin degradation and in providing composition and sequence information (Linhardt et al., 1990). F. he~ l., . produces at least three types of heparinsl~es (I, II and III) with different substrate specificities (Lohse &
30 Linhardt, 1992). It has been proposed that all three enzymes cleave heparin through an elimination reaction catalyzed by a nucleophilic amino acid.
-CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 Hep~rin~e I (or heparin lyase I, EC 4.2.2.7) is a 42,500 Da enzyme isolated from the periplasm of F. h~inulll which cleaves heparin specifically in a random endolytic fashion (Linker and Hovingh, 1972; Linhardt et al., 1982) at linkages of the type HNS 6X-I2S or HNS,6S-I2X~ where X is either sulfated or unsubstituted (Linhardt, et al., 1990; Desai, et al., 1993). The 5 characteristic heparin degradation product profile includes ~U2SHNs (disaccharide l);
t~U2SHNs6s (disaccharide 2), ~u2sHNsI2sHNs6s (tetrasaccharide 1), ~U2SHNS6SGHNS6S
(tetrasaccharide Z), ~U2s HNS 6S I2S HNS 6S (tetrasaccharide 3), and ~U2SHNS 6SIHNAc 6SGHNS 3S 6S
(hçx~echaride)~
~ep~rin~se I has recently been cloned and ~ ssed in E. coli (Sasisekharan et al., 10 1993). The enzyme has been utilized in the sequence d~e. . l~ i. .;-l ion of sugars, in the preparation of small heparin fragments for th~ldl ~;ulic uses, and in the ex vivo removal of heparin from blood (Linhardt et al., 1990; Bernstein et al., 1988). Extracorporeal medical devices (e.g. hemodialyzer, pump-oxygenator) rely on systemic hep~illi;GdLion to provide blood compatibility within the device and a blood filter cont~ining immobilized hep~rin~e I
15 at the emll~nt which is capable of neutralizing the heparin before the blood is returned to the body (Bern~tein et al., 1988).
It has been suggested that heparinase I binds heparin through Iysine residues on the enzyme surface (Yang et al., 1985; Linhardt et al., 1982). The importance of Iysines in enzyme activity is suggested by the observation that modification by amine-reactive reagents 20 and immobilization of h~hlase I on amine-reactive supports result in ~Lellsive activity losses (Comfort et al., 1989, Leckband & Langer, 1991; Bern~t~?in et al., 1988). Further evidence for an electrostatic nature of the interaction lies in the PH and ionic strength dependence of heparinase activity (Yang et al., 1985). Additionally, the finding that tetrasaccharides are the smallest heparin ~zl~nent.c that still retain substrate activity gives 25 some information about the size requirements of the active site (Linhardt et al., 1990).
Despite these ol:~s~,l v~LLions, information concerning the structure of the enzyme has been scant.
There has been much speculation in the art about the possibility of creating "cleci~ner"
enzymes, rationally ~ie~ipned to have desired substrate specificities and activities, and 30 heparinase I would be an a~lopl iate starting point for the rational design of novel polysaccharide lyases. Yet, although the importance of different levels (primary, secondarv, CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 and tertiary) of protein structure in det~ -g the functional activity of enzymes has long been ~ecognized, the lack of a broad and detailed underst~n-lin~; of the rel~ti~ n~hip between structure and function has prevented significant progress. Even for enzymes which have known activities, substrates, and primary structures, the general lack of information about 5 secondary and tertiary structures and the relationship of these to function has made it difficult to predict the functional effect of any particular changes to the primary structure.

Snmm~ry of the Invention The present invention provides for new polysaccharide lyases derived from heparinase 10 and rationally designed based upon detailed structural and functional characterization of heparinase I. In particular, in one series of embodiments, the present invention provides substantially pure polysaccharide lyases comprising the amino acid sequence of the mature hep~rin~e I protein of F. he~ ulll in which at least one amino acid residue has been substituted and in which the substitution is (a) a substitution of a cysteine residue 15 corresponding to position 135 of SEQ ID NO: 2 with a residue selected from the group co~ tinp; of a~ u L~l~, glnt~m~t~7 serine, threonine, and histidine; (b) a conservative substitution of a residue of a Cardin-Weintraub-like heparin-binding sequence XBBXXXBXB corresponding to positions 197-205 or 208-212 of SEQ ID NO: 2 with a residue which conforms to the heparin-binding sequence; (c) a conservative substitution of a 20 residue of an EF-hand-like calcium binding sequence corresponding to positions 206-220 of SEQ ID NO: 2 with a residue which conforms to the calcium binding sequence; (d) a conservative ~ub,LiLuLion of a residue of a PB1, PB2 or PB3 ~-sheet domain of SEQ ID NO:

2; (e) a non-conservative substitution of a cysteine residue corresponding to position 297 of SEQ ID NO: 2; (f) a non-conservative substitution of a residue of a PB1, PB2 or PB3 ~B-sheet 25 domain of SEQ ID NO: 2 which preserves a parallel 13-helix tertiary structure characteristic of SEQ ID NO: 2;(g) a deletion of one or more residues of a N-termin~l region or a C-t~rrnin~l ~ region of SEQ ID NO: 2 which preserves a parallel ~3-helix tertiary structure characteristic of SEQ ID NO: 2; or (h) a non-conservative substitution of a serine residue corresponding to position 39 of SEQ ID NO: 2.
The present invention thus contemplates any of the foregoing substitutions alone, but also contemplates combinations of these substitutions which result in functionally active CA 0223~223 1998-04-29 modified hep~rin~ees with altered stability, activity, and/or specificity as described in greater detail below.
It is, for example, a particular object of the invention to provide substantially pure polysaccharide lyases based upon heparinase I in which the cysteine residue corresponding to 5 position 135 of h~inase I has been substituted with an aspartate, glllt~m~te, serine, threonine, or histidine.
It is, for example, another particular object of the invention to provide substantially pure polysaccharide lyases based upon heparinase I in which the serine residue corresponding to position 39 of heparinase I has been substituted with an alanine residue.
It is, for example, another particular object of the invention to provide sllhst~nti~lly pure polysaccharide lyases based upon hep~rin~e I in which a residue of a Cardin-Weintraub-like heparin binding sequence XBBXXXBXB corresponding to positions 197-205 or 208-212 of heparinase I has been cons~l v~Lively substituted with a residue which conforms to the heparin binding sequence. In a preferred set of emborliment~, the conservative substitution is 15 of a lysine residue corresponding to position 198,199 or 205 of hep~rin~ce I with an arginine or hi~ti~1ine, most preferably an arginine. In other plcr~ d embo~liment~, the conservative substitution is of the histidine residue corresponding to position 203 of heparinase I.
It is, for example, yet another particular object of the invention to provide substantially pure polysaccharide lyases based upon heparinase I in which a conservative substitution of a residue of an EF-hand-like calcium binding sequence corresponding to positions 206-220 of hep~ e I with a residue which conforms to the calcium binding sequence has been made. In ~lt;r~ d embo~liment~, the ~llbstitlltion is of a lysine residue corresponding to position 208, 209,211 or 214 of heparinase I with an arginine or histidine, preferably an arginine. In other ~lc;r~ ,d embo-limentc, the substitution is of an aspartate residue corresponding to positions 210 or 212 of hep~rin~ce I with a glllt~mz~te.
According to another aspect of the invention, there is provided a high order lowmolecular weight heparin fragments greater tan he~ ceh~rides obtainable by the process of incubating with heparin the substantially pure polysaccharide lyase of the invention (described above) to produce the low molecular weight heparin fragment. The low molecular weight heparin fr~gment~ can be separateded on an anionic exchange chromotography column (such as a POROS column from PerSeptive Biosystems).

CA 0223~223 1998-04-29 _ 5 _ According to another aspect of the invention, there is provided a ph~rm~reuticalplep~dlion comprising a sterile formulation of the substantially pure polysaccharide lyase of the invention (described above) and a ph~rm~reutically acceptable carrier.
According to another aspect of the invention, there is provided methods for treating 5 subjects in need of depletion of circulating heparin. Effective amounts of the polysaccharides of the invention are ~flmini~ered to subjects in need of such treatment.
According to another aspect of the invention there is provided an isolated nucleic acid encoding the subst~nti~lly pure polysaccharide lyase of the invention. This aspect of the invention also includes nucleic acids which hybridize under stringent hybridization conditions to 10 the isolated nucleic acid of SEQ ID NO 1 or to the complement of the nucleic acid of SEQ ID
NO 1 and which are modified to encode a modified heparinase as describedabove, and nucleic acids that differ from the nucleic acids ub codon sequence due to the degeneracy of the genetic code.
The invention further provides a recombinant host cell including any of the isolated 15 nucleic acids of the invention.
The invention further provides an ~x~Le~ion vector including any of the isolated nucleic acids of the invention.
According to another aspect of the invention there is provided a method of removing active heparin from a heparin co,.l~i..i,.g fluid. The method involves the step of contacting a 20 heparin colll 1;llillg fluid with the substantially pure polysaccharide lyase ofthe invention. In one embodiment of the invention the substantially pure polysaccharide lyase is immobilized on a solid support.
In another series of embo-limentc, the present invention provides new polysaccharide lyases in which non-conservative substitutions have been made. Thus, these embo~1iment~
25 include subst~nti~lly pure poly~rçhzlride lyases based upon hepd,;llase I in which at least one amino acid residue has been substituted and in which the substitution is (a) a substitution of a cysteine residue corresponding to position 135 of heparinase I with an a~lal~, glnts~m~te, serine, threonine or histidine residue, (b) a substitution of a histidine residue corresponding to CA 0223~223 1998-04-29 position 203 of heparinase I with an a~u L~ , glut~m~te, serine, l~ o~ e or cysteine; (c) a substitution of a lysine residue corresponding to position 198, 199, 205, 208, 209, 211 or 214 of hep~rin~ee I with a small non-polar amino acid, a small polar amino acid, or an acidic arnino acid, (d) a substitution of a small polar or small non-polar amino acid for a residue corresponding 5 to the Phel97, Asn200, Asp204, Glu207, Asp210, Asp212 or Gly213 of heparinase I.
In this series of embo-1iment.c, the present invention provides for single substitutions and also provides for polysaccharide lyases with combinations of these substitutions as discussed above.
In another series of embodiments, the present invention provides for a modified 10 heparinase having a modified heparinase kCat value, wherein the modified heparinase k~ at value is s75% of a native heparinase kCat value of a complementary native hep~rin~ce The complementary native heparinase for modified hep~rin~e I is, of course, heparinase I.
In another series of embofiimente t_e modified heparinase is immobilized on a solid support membrane.
In another series of embo-iimente7 the present invention also provides for polysaccharide lyases in which the overnight heparin degradation activity is less than about 75% of that of native hep~rin~ee I.
In another series of embo-limente, the present invention also provides for polysaccharide lyases in which the clegrzl~tion product profile is altered from that of native heparinase I. In one 20 embodiment the polysaccharide lyase is a modified heparinase I having a modified product profile, wherein the modified product profile of the modified heparinase I is ~50% similar to a native product profile of a native hep~rin~ee I. In another embodiment the substzlnti~lly pure polysaccharide lyase is a modified heparinase I producing when contacted with heparin less than 20% of disaccharide 1 and trisaccharides 2 and 3 as col"p~L-d to native heparinase I when 25 cf-nt~cted with the heparin.
In another series of embodiments, the present invention also provides active fr~gm~nte and functionally equivalent variants thereof of the polysaccharide lyases of the invention that have substantially the same heparinase I activity as the substituted polysaccharide lyases of the invention.

CA 0223~223 1998-04-29 W O 97/16~56 PCTAUS96/17310 ~rief I)eser~ption of the Dr~wi. ~.~
~ Figure 1 presents a "side" view of the parallel ,B-sheet structure of the core of heparinase I
in which Cysl35 is marked by an arrow.
Figure 2 presents a view "down" the axis of the parallel ~-helix of the core of heparinase I
in which Cysl35 is marked by an arrow.
Figure 3 shows a heparin tetrasaccharide bound in the heparin binding domain. Cysl35 and His203 are in close ~1~ xhlliLy to each other and the hydrogen of the iduronate marked by an arrow.
Det:~iled D~ lion of the Invention The present invention provides a series of new polysaccharide lyases derived from the hep~rin~e I (heparin lyase I, EC 4.2.2.7) of F. he~ dlhlulll. In particular, based upon a detailed structural and functional characl~l;~Lion of heparinase I, new polysaccharide lyases with altered 15 stability, activity and specificity are provided.
The nucleotide and amino acid sequences of heparinase I are provided in SEQ ID NO: 1 and SEQ ID NO: 2, respectively. These sequences were reported in S~ei~kh~ran, et al. (1993) and provided the first insight into the primary structure of the native hep~rin~e I of hel~a ~
The present disclosure provides a wealth of additional information about the secondary and tertiary structure of this polysaccharide lyase as well as information relating to the functional roles of the various regions of the enzyme. This information is based upon detailed bioc~.hemic~l mapping of the active site and polysaccharide binding domain, characterization of these sites through kinetic studies, chara ;L~fi;~a~ion of m~lt~nt~ created by site-directed mutagenesis, and colllpuLt;l-based modeling of secondary and tertiary structures. The result is a detailed picture of the primary, secondary, and tertiary structures of heparinase I and the functional roles of various regions of the enzyme.

CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 Using this detailed knowledge of the native heparinase I of F. h~ . ., the present disclosure provides novel, rationally designed polysaccharide lyases, methods of ~lesi~ninp and producing such lyases, and uses therefor.
Heparinase I has a typical prokaryotic leader sequence and cleavage site. This leader 5 sequence corresponds to residues 1-21 of SEQ ID NO: 2. A recombinant construct lacking the leader (L) residues"l~si~n~t~l -L r-hepz~rin~e I, has been expressed in a pET plasmid and the recombinant enzyme is still as active as the native F. heparinllm hep~rin~e, inrlic~finp that these residues are not essential for enzymatic activit,v. Inclusion of the leader in the mature protein, however, does not interfere with the enzyme's activity (~ kh~ran et al., 1993).
Although the full heparinase I amino acid sequence includes three cysteines, one of these (at position 17 of SEQ ID NO: 2) is in the leader sequence. Therefore, the mature heparinase I
has two cysteines. These cysteines are at positions 135 ("Cysl35") and 297 ("Cys297") of SEQ
IDNO: 2.
Previous studies had suggested that the two cysteine residues of mature hep~rin~e I form a ~ c-llfille bridge. Comfort et al. (1989), for example, compared the activity of heparinase I in which the cysteine residues had been reduced with heparinase in which the cysteines had not been altered. These experiments showed that the reduced heparinase I had lower activity than the native hep~rin~e I. Therefore, it was suggested that the two cysteine residues may form a disulfide bridge in native hepz~rin~e I and that the disulfide bridge may be important to m~;"~ i"g tertia~y structure and activity.
Studies using sulfhydryl modifications, kinetics of enzyme inactivation, and colllpetiLive inhibition of inactivation were performed by the present inventors to dçt~rmine the functional roles of the two cysteines in catalysis. Purified heparinase I ~ ald~ions (Example 1) were modified with various sulfhydryl specific reagents to map and characterize the cysteine residues.
We now disclose (a) that the two cysteines of hep~rin~e I do not form a disulfide bridge but, rather, are located in different parts of the tertiary structure with different microenvironment~, (b) that Cysl35 is surface-accessible, (c) that Cysl35 is in the active site, (d) that the microen~h~l"llent around Cysl35 is positively charged, and (e) that Cysl35 is involved CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 _ g _ in catalysis. In contrast, Cys297 is buried in the hydrophobic core of the protein and is not essential to hep~rin~e I activity. See Examples 2-8.
To further demonstrate that Cysl35 is an active site cysteine involved in catalysis and that Cys297 is not ec~nti~l to enzyme activity, recombinant polysaccharide lyases were produced in ~ 5 which these residues were modified. Using site-directed mutagenesis, Cysl35 was replaced by the more weakly nucleophilic residue serine, by the charged residues hi~ti~ine, gl~ and aspartate, and by the neutral alanine. Replacement of Cysl35 by aspartate, glnt~m~te7 serine or histidine led to decreases in activity (kC~t values of approximately 3.5%,3.8%, 2% and 3%, respectively, of the kCat of native heparinase) and replacement with the neutral alanine abolished activity. Importantly, the cleavage specificity of the recombinant lyases was unaffected.
Replacement of Cys297 with either serine or alanine had no effect on activity. See Example 9.
Next, we investigated the heparin-binding domain of heparinase I using activity analysis at varying calcium concentrations, heparin affinity chromatography, affinity co-electrophoresis, hep~rin blotting of CnBr digests, co~ iLive binding and blotting of tryptic digests, competition with a synthetic binding domain peptide, PCMB protection and tryptic digests, and site-directed mutagenesis ofthe binding dom~in See Examples 10-17.
We now disclose that (a) heparinase I possesses a lysine-rich heparin binding domain e~ten~ling appr~ imzltely from residues 195-220 of SEQ ID NO.:2, (b) that the binding domain possesses two "Cardin-Weintraub" heparin binding sequences at approximately residues 197-205 and 206-212, (c) that heparinase activity is calcium dependent and the heparin binding domain contains an EF-hand-like calcium binding site at appro~im~tcly residues 206-220, and (d) that the heparin binding domain is in close proximity to Cysl35 in native heparinase I.
As noted above, the heparin binding domain possesses two sequences which almost conform to consensus sequences found in many heparin binding proteins (Cardin and Weintraub, 1989). The Cardin-Weintraub sequence is of the form XBBBXXBX or XBBXBX (where B is any basic residue and X is any hydrophobic or other residue). The heparinase I sequences which nearly conform to these sequences are found at positions 197-205 and 206-212 of SEQ ID NO.:2.
Using site-directed mutagenesis, recombinant proteins were produced in which these sites were CA 0223~223 1998-04-29 W O 97/165~6 PCT~US96/17310 - 10- _ altered. A third Cardin-W~;hlLldub sequence, at ~ lo~illlately positions 331-337, does not appear to be involved in heparin binding.
Also within the heparin binding domain is a sequence which nearly conforms to an EF-hand calcium binding domain (Kretsinger et al., 1991) at positions 206-220. The EF-hand 5 consensus sequence is shown in Table II. Substitutions conforrning to an EF-hand calcium binding con~n~ sequence, but which would not conform to a Cardin-Weintraub heparin binding sequence, appear to be tolerated but a deletion of the entire sequence leads to enzyme inactivity. For example, s~lhstil~tion of both Lys208 and Lys209 with the similarly positive arginine led to a 40% decrease in initial activity (kcat) but had no effect on the product profile.
10 This substitution is consistent with both the EF-hand and Cardin-Weintraub consensus sequences. Substitution of both of these residues with the neutral alanine did not significantly alter the product profile but led to a 76% decrease in kC"t. This substitution conforms to the EF-hand consensus but not the Cardin-Weintraub con~Pn~n~. Moreover, substitution of both lysines with negative a~3~ L~le residues results in a decrease in kcat of only 46% and an unaltered product 15 profile, further showing that the amines of these lysine residues are not necessary for catalysis.
Therefore this stretch of the sequence is primarily a calcium binding site and, secondarily, a heparin binding sequence. Deletion of this region abolishes activity, suggesting either that calcium is necess~ to activity or that the deletion disrupts the tertiary structure of the active site.
A second EF-hand ~1om~in, at approximately positions 372-384, does not appear to be involved 20 in catalysis.
With respect to the heparin binding site at residues 197-205, a dirr~ L picture emerges.
This sequence nearly conforms to a Cardin-Weintraub heparin binding sequence, having the motif XBBX~BXB. This sequence does not conform to an EF-hand calcium binding site.
Substitution of positively charged arginines for lysines (Lysl98 and Lysl99) conserves the 25 Cardin-Weintraub-like motif and results in a 46% decrease in kcat but no change in product profile. Interestingly, substitution of Lys 198 and Lys 199 with either the neutral alanine or negatively charged aspartate does not abolish activity but, rather, results in lower activity (k~at 4.1 % of wild type) and an altered product profile. Another basic residue in this domain, His203, ~pe~u~ to be involved in the active site as an acid/base catalyst. Substitution of His203 with CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 nucleophilic negative or polar residues which do not conform to the Cardin-Weintraub sequence (e.g., as~ L~, serine or cysteine) does not inactivate the enzyme but, rather, results in a lyase - with decreased activity (k~"t 3-4% of wild type). Substitution with the neutral ~l~nin~-7 however, abolishes activity, suggesting that this residue may be important in proton transfer.
~ 5 Using the information relating to the active site and heparin binding domain of heparinase I, in conjunction with computer ~l~t~h~e searches for homologous sequences of known structure, co~ ulel programs for the prediction of secondary structures, and conl~ule~ tet1 modeling, we have developed a model of the tertiary structure of native heparinase I.
We now disclose that heparinase I is characterized by a parallel 13-helix structure. A
similar structure has recently been reported for two pectate lyases (Yoder et al., 1993). For much of this structure, each turn of the helix consists of two or three ~-strands separated by non-,B
stretches. The turns of the helix are stacked such that the ,l~-strands of adjacent turns may form parallel ,(~-sheets. Thus, the helix is three-sided for most of the core structure with the three sides consisting largely of three parallel ,l~-sheets. The three parallel ,B-sheets forming the sides of the helical core are clesi~n~f~l PB1, PB2, PB3. In each turn, the ,I~-strands are between two and seven residues in length and each turn includes a minimum of seventeen residues and an average of about nine residues in ~-strands. Between ~-strands are loops of varying lengths. Both Cysl35 and the heparin binding domain are found in such loops. Table I discloses the approximate positions of the residues of heparinase I which are found in the ,B-strands and to which of the ~-sheets each ,I~-strand belongs. Seh~?m~tic views of the scaffold of Table I, omitting some of loops between ,B-strands, are presented in Figures 1 and 2. Figure 1 presents a "side" view in which Cysl35 is marked by an arrow. Figure 2 presents a view "down" the axis of the parallel ~-helix and, again, Cysl 35 is marked by an arrow.
Note that the active site cysteine, Cysl35, is located in a non-~-stretch between PBl and PB2. This is consistent with the results of the sulfhydryl modification t~ e~ .ent~ which indicated that Cysl35 is surface ~rcç~ihle. Cys297, on the other hand, is part of a ~-strand in PB 1 and its side chain is believed to be directed toward the hydrophobic interior of the helix.
The heparin binding domain loops out of a turn between PB3 and PB 1 and extends back up the ~-helix toward Cysl35. This structure places the active site cysteine in proximity to the heparin CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 binding domain and explains the positively charged micro~ vhon~llent of Cysl35 and the inhibition of t_e PCMB reaction with Cysl35 by the addition of heparin.
From the results disclosed herein, a molecular mech~ni~m for the interplay between heparin binding and catalysis by heparinase I emerges. Cysl35 is catalytically active, but is not a 5 determin~nt for heparin binding, since chemically derivatizing it did not affect heparinase binding to heparin. It is proposed that this residue abstracts the C5 proton on the uronate of the cch~ride repeat unit of the acidic poly~c(~h~rides~ and initiates the elimin~tion based depolymerization reaction. The thiol group of cysteine has a pKa of 8.35 in free solution (Fresht, 1985), indicating that this residue will be fully ~ t~ndLed at pH 7.0, the pH op~ ull for 10 hep~rin~e I (Yang et al., 1985). A positively charged environment from nearby lysines or ar~inine-C7 however, will tend to keep the thiol group negatively charged (i.e. lowering its pK") so that it can act as a base for proton abstraction. This would account for the preferential reactivity of Cysl35 with negatively charged reagents and the high reactivity of Cysl35 at pH 6.5 (Example 6).
The heparin binding domain (residues 195-220) controls enzymatic selectivity in terms of substrate size, and the hi.~ti~line from this region (His203) also assists the catalytic mech~ni~m, possibly by acting as a secondary nucleophile or as an ec~çnti~l amino acid in a possible "proton relay system." This site also contains the calcium co-ordination site which bridges heparin to heparinase through calcium, and perhaps orients the functional group(s) of the uronate to the 20 active site region involving Cysl35 and His203. The heparin binding site and the basic residues close to Cysl35 (e.g., Lysl32, Argl41, etc.) together constitute a heparin binding domain in hep~rin~e I that provide the basic environment for Cys 135. Substitution of lLysine 132 to an alanine residue reduced the activty of the h~prin~ee (see table IV). This positive charge enviromnent around the surface ?ccç~ihle Cysl35 enhances the reactivity ofthis thiol residue.
25 Thus, we postulate that a positively charged heparin binding domain spatially close to Cysl35 provides the necessary charge compl~ment~rity for very specific heparin binding on the one hand, while on the other it provides for the active site environment which plays a key role in biasing the active site reactivity. Figure 3 shows a schem~tic representation of the active site of heparinase I with a heparin tetrasaccharide bound in the heparin binding domain. Cysl35 and CA 0223~223 1998-04-29 His203 are in close proximity to each other and to the hydrogen of the iduronate m~rk~1 by an arrow.
In light of the present disclosure, one of ordinary skill in the art is now able to rationally design new polysaccharide lyases with altered activity and specificity. In particular, one is able 5 to design lyases with altered activity by the modification of Cysl35 or the positively charged residues surrounding it in the active site or the heparin binding cl- m~in In addition, one is enabled to design modified polysaccharide lyases with altered specificity by modification of the residues of the Cardin-Wei~ dub-like sequence in the heparin binding domain. Finally, one is able to produce various other novel polysaccharide lyases in which non-es~e~-ti~l residues are 10 freely changed or substituted conservatively.

Pr~f~ d Embodiments The present invention provides for novel polysaccharide lyases rationally designed on the basis of the sequence of the heparinase I of F. heparinum and the structural and functional 15 characterizations disclosed herein.
In the description that follows, reference will be made to the amino acid residues and residue positions of native heparinase I disclosed in SEQ ID NO: 2. In particular, residues and residue positions will be referred to as "corresponding to" a particular residue or residue position of heparinase I. As will be obvious to one of oLdhl~ ~ skill in the art, these positions are relative 20 and, therefore, insertions or deletions of one or more residues would have the effect of altering the numbering of downstream residues. In particular, N-termin~l insertions or deletions (e.g., deletion of one or more of the 21 N-t~rmin~l leader sequence residues) would alter the numbering of all subsequent residues. Therefore, as used herein, a residue in a recombinant polysaccharide lyase will be referred to as "corresponding to" a residue of the full heparinase I if, using standard 25 sequence comparison programs, they would be aligned. Many such sequence ~lignment programs are now available to one of ordinary skill in the art and their use in sequence colllpalisons has become standard (e.g., "LALIGN" available via the internet at http://genome.eerie.fr/fasta/). As used herein, this convention of referring to the positions of residues of the recombinant polysaccharide lyases by their corresponding heparinase I residues CA 0223~223 1998-04-29 shall extend not only to embo-1imentc including N-t~rmin~ insertions or deletions but also to ;ntern~l insertions or deletions (e.g, insertions or deletions in "loop" regions).
In addition, in the description which follows, certain substitutions of one amino acid residue for another in a recombinant polysaccharide lyase will be referred to as "conservative substitutions." As used herein, a "conservative amino acid substitution" or "consel v~liv~
substitution" refers to an amino acid substitution in which the ~ub~iLuled amino acid residue is of similar charge as the replaced residue and is of similar or smaller size than the replaced residue.
Conservative substitutions of amino acids include substitutions made amongst amino acids within the following groups: (a) the small non-polar amino acids, A, M, I, L, and V; (b) the small 10 polar amino acids, G, S, T and C; (c) the amido amino acids, Q and N; (d) the aromatic amino acids, F, Y and W; (e) the basic amino acids, K, R and H; and (f) the acidic amino acids, E and D.
Substitutions which are charge neutral and which replace a residue with a smaller residue may also be considered "conservative substitutions" even if the residues are in different groups (e.g., replacement of phenyl~l~nine with the smaller isoleucine).
Additionally, some of the amino acid substitutions are non-conservative substitutions. In certain embo-limentc where the substitution is remote from the active or binding sites, the non-conservative substitutions are easily tolerated provided that they preserve the parallel B-helix tertiary structure characteristic of native hep~3rin~ce (SEQ ID NO: 2), thereby preserving the active and binding sites.
As shown in the experimental examples below and, in particular Table TV, the present invention provides a variety of novel polysaccharide lyases with heparin-cleaving activity in which the initial activity or kcat iS reduced relative to the kcat of native heparinase I. For each of the novel polysaccharide lyases tested thus far, the kcat of the recombinant lyase is less than about 75% of that of native hPp~. ;. ,~ce I. Such lyases have particular utility as substitutes for 25 hepalillase I in the controlled degr~ tion of heparin and other polysaccharides because the reaction proceeds at a slower rate. Table IV also shows the percentage of degradation products, relative to native hep~rin~ce I, produced by these new lyases after overnight incubation with heparin. In all cases but two, discussed below, the product profile of these new lyases is eccenti~lly identical to the characteristic heparinase I product profile.

CA 0223~223 1998-04-29 W O 97/165S6 PCT~US96/17310 The novel polysaccharide lyases of the invention are rationally f~igne-l based upon the sequence of heparinase I and have at least one amino acid substitution at the active site Cysl35, ~ in the first Cardin-Weintraub-like sequence in the heparin binding domain, or in the EF-hand-like calciurn binding sequence in the heparin binding domain. With respect to Cysl35, the S substitutions are preferably substitutions of nucleophilic or negatively charged residues which can replace the functional role of Cysl35 in catalysis. With respect to the Cardin-Weintraub-like and EF-hand-like sequences, the substitutions are preferably conservative substitutions which preserve the motif of the sequence but, as shown in the examples below, these substitutions need not be conservative in order to m~int~in enzymatic activity.
Thus, as a first plert;-l~d embodiment, the present invention provides a novel polysaccharide lyase comprising the mature peptide amino acid sequence of SEQ ID NO: 2 (i.e.
residues 22-384) in which the residue corresponding to Cysl35 has been substituted by a serine, histidine, glllt~m~te or aspartate residue. Recombinant lyases with such a substitution have been found to have reduced initial activity (kCa~ and have particular utility when partial or slower 15 heparin degradation is desired. Such recombinant polysaccharide lyases may optionally include the heparinase leader sequence or may include any of the other modifications described herein.
In another set of embo-liment~, the present invention provides novel polysaccharide lyases comprising the mature peptide amino acid sequence of SEQ ID NO: 2 in which one or more of the residues of the Cardin-Weintraub-like sequence, XBBXXXBXB, corresponding to 20 positions 197-205 are substituted. For example, one or more of the lysine residues corresponding to positions 198, 199 or 205 of the heparin binding domain may be substituted by other positively charged residues. Such substitutions m~int~in the positively charged microenvironment necessary for heparin binding and catalysis by Cysl35. These substitutions may be conservative, such as replacing one or more of the two lysine residues (corresponding to positions 198 and 199 25 or SEQ ID NO: 2) with an arginine or histidine. Repl~- ement of both of these residues with arginine leads to the creation of a lyase with 60% the kCat of native heparinase I. Altern~tively, - one or more of these lysines may be substituted with a small polar, small non-polar or even an acidic amino acid residue to produce a lyase with reduced activity. For example, recombinant lyases with both of these lysines replaced by alanine or aspartate have been shown to retain CA 0223~223 1998-04-29 catalytic activity but have kCat values only about 4% of the native heparinase I. The lysine corresponding to position 205 of SEQ ID NO: 2, also may be modified. Substitution with an arginine or hi~titline is one preferred embodiment. Alternatively, this residue may be substituted with a small polar, small non-polar or acidic amino acid residue. Substitution of one of these 5 residues with a much larger residue (e.g. tyrosine), however, abolishes activity. As noted above, the histidine at position 203 of heparinase I appears to be involved in the active site as an acid/base catalyst. Replacement of this residue by a neutral residue (e.g. alanine) abolishes catalytic activity. This residue may, however, be substituted, by serine, cysteine, threonine, or even the negative a~l~ L~l~ or glllt~m~t.- to produce a polysaccharide lyase with a reduced k The non-basic residues in the region corresponding to this first Cardin-Weintraub-like sequence may also be modified while preserving the XBBXXXBXB motif by m~king conservative substitutions. In order to m~int~in heparin binding ability, the substitutions are preferably conservative with respect to residue size (e.g. Phel97 - Tyr; Ile201 - Leu) and charge (e.g., Ala202 - Gly, Asp204 - Glu). AltPrn~tively, small polar or small non-polar residues may be substituted for any of these residues. The residue corresponding to Asn200 in SEQ ID NO: 2, for example, may be changed to a glutamine to produce a recombinant Iyase. Substitution of Asn200 with alanine results in a recombinant Iyase with a kCat of approximately 48% wild-type.
The substitution of this asparagine with a Iysine residue, however, is not tolerated because it is not a conservative substitution with respect to size (i.e. Iysine is larger than asparagine).
In another set of embo-liment~, novel polysaccharide lyases are provided comprising the mature peptide amino acid sequence of SEQ ID NO: 2 wherein one or more residues corresponding to the EF-hand-like calcium binding domain (residues 206-220) have been substituted but calcium binding ability and catalytic activity is retained. Preferably, these ~,ub~,LiLuLions are conservative with respect to size and charge. Thus, one or more of the lysines co~ pollding to positions 208, 209, 211 or 214 may be substituted with arginine or histidine.
~ltern~tively, one or more of these residues may be substituted with a small polar or small non-polar residue. For example, replacement of Lys214, which is not constrained in the EF-hand motif, with Ala resulted in a Iyase with 60% of the kCat of the wild type. The aspartate residues corresponding to positions 210 and 212 of SEQ ID NO: 2 are constrained in the EF-hand CA 0223~223 1998-04-29 sequence motif. Replacement of these residues by ghltz-m~t~, however, would conform with the motif and would also constitute a conservative substitution with respect to charge and - a~p~ imate size. Conservative substitutions of the neutral residues of this region may also be made as well as substitutions with small polar or small non-polar residues.
The EF-hand-like calcium binding domain has also been shown to be tolerant to some substitutions which do not conform to the EF-hand motif. Thus, for example, the substitutions of Glu207 ~ Ala, Asp210 ~ Ala, Asp212 -Ala, and Gly213 - Ala do not destroy catalytic activity but result in lyases with kCat values of 18%, 50%, 50%, and 20%, respectively, of the k~,t of native heparinase I. As with the Iyases with modified heparin binding domains, these recombinant 10 lyases with reduced kCat have utility in that they allow for slower and more controlled degradation of heparin and other polysaccharides. In some cases double and triple mutations in the EF-hand region produce novel polysaccharide lyases having even lower enzymatic activity.In another embodiment a novel polysaccharide lyase is provided which retains all of the enzymatic activity ofthe heparinase I but which is not immunogenic when ~timini~t~red to a 15 subject. This novel polysaccharide lyase is produced by making a non-conservative substitution of the serine at position 39 of heparinase I which removes the gycosylation site of heparinase I.
The novel substituted polysaccharide lyase is not immlmngenic because the immlln~genic region (glycosylation) of the lyase is removed. Preferably the serine residue corresponding to position 39 of hc~p~illase I is substituted with an alanine residue.
In one particular embodiment, the present invention provides novel polys~ççh:-ride lyases in which the product profile is different from that of native heparinase I. In particular, polysaccharide lyases compri~in~ the mature peptide amino acid sequence of SEQ ID NO: 2 in which the residues corresponding to Lysl98 and Lysl99 have been replaced by negatively charged residues (i.e. Asp or Glu) produce less than 20% and, in fact, only neglipihle amounts of 25 the char~çt~ri~tic disaccharide 1, tekasaccharide 2 and tetrzl~cçh~ride 3 of the hep~rin~e I
product profile. Relative to heparinase I, these recombinant lyases, after overnight incubation ~ with heparin, produce about 50% of the characteristic disaccharide 2 and tetrasaccharide 1.
These lyases have particular utility in the sequencing of heparin and other complex polysaccharides .

CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 The product profile produced by the novel polys~cf~h~ride lyases includes high order low moleuclar weight h~p~rin fr~gment~ which are not included in the product profile produced by native hep~rin~ee I. The high order low molecular weight fr~gment~ are large undigested fr~gment~ of heparin which have various levels of therapeutic activity attributed to larger fr~ment~ of heparin.
In another set of embo-lim~nt~, the invention provides novel polysaccharide lyases comprising the mature peptide amino acid sequence of SEQ ID NO: 2 in which one or more residues outside of the active site and heparin binding domain have been substituted so as to ~les~l vt; the overall tertiary structure of the enzyme. In particular, polysaccharide Iyases in 10 which conservative s--bstitlltions of any of the residues of the ~-strands of Table I are contemplated. Because these residues are now known not to be involved in catalysis, and because a basic model of the tertiary structure of heparinase I is now disclosed, such conservative substitutions may be made without undue experiment~tion and with a high expectation of success. In a particularly pl~rt;--~,d embodiment, the residue corresponding to Cys297 may be 15 substituted by a small polar or non-polar residue (e.g., Cys297 - Ser or Cys297 - Ala) without affecting enzyme activity. Although the Cys297 residue has now been shown to be irrelevant to protein activity, modification of this residue is particularly contemplated in ~.~r~ ,d embodiments to increase stability and simplify mass production and purification by removing the possibility of ullw~ulL~d disulfide cross-linking with Cysl35.
The substantially pure polysaccharide lyase of the invention may also be used to remove active heparin from a heparin co..~ fluid. A heparin conts~inin~ fluid is collt~te~l with the subst~ntiAlly pure polysaccharide Iyase of the invention to degrade the heparin. The method is particularly useful for the ex vivo removal of heparin from blood. In one embodiment of the invention the subst~nti~lly pure polysaccharide lyase is immobilized on a solid support as is 25 conventional in the art. The solid support co..~ g the immobilized polysaccharide lyase may be used in extracorporeal medical devices (e.g. hemodialyzer, pump-oxygenator) in which systemic ht;~ ;on to prevent the blood in the devise from clotting. The support membrane cont~inin~ immobilized heparinase I is positioned at the end of the devise to ne~ltr~li7P the heparin before the blood is returned to the body.

CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 According to another aspect of the invention, there is provided methods for treating subjects in need of depletion of circulating heparin. Effective amounts of the polysaccharides of the invention are ~1mini~tçred to subjects in need of such tre~tment For example, subjects undergoing open heart surgery or hemodialysis often are in need of depletion of medically 5 undesirable amounts of heparin in blood as a result of blood as a result of the surgery or hemodialysis. The subjects may be ~(1mini~tered the modified heparinases of the invention in a manner and in amounts presently found acceptable when using native heparin. Effective amounts are those amounts which will result in a desired reduction in circulating heparin levels without causing any other medically unacceptable side effects. Such amounts can be ~lçt.ormined with no 10 more than routine eXperiment~tion. It is believed that doses ranging from 1 nanogram/kilogram to 100 milligrams/kilogram, depending upon the mode of ~flmini~tration, will be effective. The absolute amount will depend upon a variety of factors (including whether the ~1mini~tration is in conjunction with other methods of tre~tment, the number of doses and individual patient parameters including age, physical condition, size and weight) and can be cletermined with 15 routine eXperimçnt~tion. It is pler~ d generally that a m~xhll~ dose be used, that is, the highest safe dose according to sound medical j~lrlgment The mode of ~-lmini~tration may be any medically acceptable mode including oral, subcutaneous, hllldvellous, etc.
One of oldill~y skill in the art, in light of the present disclosure, is now enabled to produce substantially pure ~ ~dlions of any of these novel polysaccharide lyases by standard 20 recombinant technology. That is, one may substitute ~n~liate codons in SEQ ID NO: 1 to produce the desired amino acid substitutions by standard site-directed mutagenesis techniques.
Obviously, one may also use any sequence which differs from SEQ ID NO: 1 only due to the degeneracy of the genetic code as the starting point for site directed mutagenesis. The mllt~tecl nucleic acid sequence may then be ligated into an d~pLopl;ate expression vector and expressed in 25 a host such as F. h~ ..,l or ~. coli. The reslllt~nt polysaccharide lyase may then be purified by techniques well known in the art, including those disclosed below and in Sasisekharan, et al.
~ (1993). As used herein, the term "substantially pure" means that the proteins are essentially free of other substances to an extent practical and a~lu~liate for their intended use. In particular, the proteins are sufficiently pure and are sufficiently free from other biological con~titllent~ of their CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 hosts cells so as to be useful in, for example, protein sequencing, or producing ph~rrn~reutical dLiOnS.
In another set of embodiments an isolated nucleic acid encoding the substantially pure polysaccharide Iyase of the invention is provided. As used herein with respect to nucleic acids, 5 the term "isolated" means: (I) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) recombinantly produced by cloning; (iii) purified, as by cleavage and gel separation;
or (iv) synth~i7~l by, for example, chemical synthesis. An isolated nucleic acid is one which is readily manipulable by recombinant DNA techniques well known in the art. Thus, a nucleotide sequence contained in a vector in which 5' and 3' restriction sites are known or for which 10 polymerase chain reaction (PCR) primer sequences have been disclosed is considered isolated but a nucleic acid sequence existing in its native state in its natural host is not. An isolated nucleic acid may be subst~nti~lly purified, but need not be. For example, a nucleic acid that is isolated within a cloning or c;x~l~;,sion vector is not pure in that it may comprise only a tiny percentage of the material in the cell in which it resides. Such a nucleic acid is isolated, however, as the term is 15 used herein because it is readily manipulable by standard techniques known to those of or.lh skill in the art.
As used herein, a coding sequence and regulatory sequences are said to be "operably joined" when they are covalently linked in such a way as to place the expression or transcription of the coding sequence under the influence or control of the regulatory sequences. If it is desired 20 that the coding sequences be tr~n~l~t~-l into a functional protein, two ~NA sequences are said to be operably joined if induction of a promoter in the 5' regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA
sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) illL~
2!; with the ability of the corresponding RNA transcript to be tr~n~l~te~l into a protein. Thus, a promoter region would be operably joined to a coding sequence if the promoter region were CA 0223~223 1998-04-29 capable of effecting transcription of that DNA sequence such that the resulting transcript might be trz~n~tr~l into the desired protein or polypeptide.
- The precise nature of the regulatory sequences needed for gene e~pl~ssion may vary between species or cell types, but shall in general include, as necessary, 5' non-transcribing and 5' 5 non-tr~n~ tin~ sequences involved with initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like. Especially, such 5' non-transcribing regulatory sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined gene. Promoters may be con~ uliv~
or inducible. Regulatory sequences may also include enhancer sequences or u~ l activator o sequences, as desired.
As used herein, a "vector" may be any of a number of nucleic acids into which a desired sequence may be inserted by restriction and ligation for transport between dirr. ~ l genetic environments or for expression in a host cell. Vectors are typically composed of DNA although RNA vectors are also available. Vectors include, but are not limited to, plasmids and phagemids.
15 A cloning vector is one which is able to replicate in a host cell, and which is further ch~r~rtPri7~cl by one or more endonuclease restriction sites at which the vector may be cut in a ~l~t~rrnin~hle fashion and into which a desired DNA sequence may be ligated such that the new recombinant vector retains its ability to replicate in the host cell. In the case of plasmids, replication of the desired sequence may occur many times as the plasmid increases in copy number within the host 20 bacterium, or just a single time per host as the host reproduces by mitosis. In the case of phage, replication may occur actively during a lytic phase or passively during a lysogenic phase. An expression vector is one into which a desired DNA sequence may be inserted by restriction and ligation such that it is operably joined to regulatory sequences and may be expressed as an RNA
transcript. Vectors may further contain one or more marker sequences suitable for use in the 25 identification of cells which have or have not been transformed or transfected with the vector.
Markers include, for example, genes encoding proteins which increase or decrease either - resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 activities are detectable by standard assays known in the art (e.g., 13-galactosidase or ~lkzllin~
phosphatase), and genes which visibly affect the phenotype of L~ ro~ ed or transfected cells, hosts, colonies or plaques. Preferred vectors are those capable of autonomous replication and expression of the structural gene products present in the DNA se~ment~ to which they are operably joined.
As used herein, the term "stringent conditions" refers to parameters known to those skilled in the art. One example of stringent conditions is hybridization at 65~C in hybridization buffer (3.5 x SSC, 0.02% Ficoll, 0.02% polyvinyl pyrolidone, 0.02% bovine serum albumin (BSA), 25mM NaH2PO4 (pH7), 0.5% SDS, 2mM EDTA). SSC is 0.15M sodiurn chloride/0.lSM
sodiurn citrate, pH7, SDS is sodium dodecyl~nlI h~t~; and EDTA is ethylene ~ mine tetra acetic acid. There are other conditions, reagents, and so forth which can be used, which result in the same degree of stringency. A skilled artisan will be f~mili~r with such conditions, and thus they are not given here. The skilled artisan also is f~mili~r with the methodology for screening cells for expression of such molecules, which then are routinely isolated, followed by isolation of the pertinent nucleic acid. Thus, homologs and alleles of the ~ub~L~ulLially pure polysaccharide Iyases of the invention, as well as nucleic acids encoding the same, may be obtained routinely, and the invention is not int~-n~led to be limited to the specific sequences disclosed.
For prokaryotic systems, plasmid vectors that contain replication sites and conkol sequences derived from a species compatible with the host may be used. Examples of suitable plasmid vectors include pBR322, pUC18, pUC19 and the like; suitable phage or bacteriophage vectors include ~gtlO, ~gtl 1 and the like; and suitable virus vectors include pMAM-neo, pKRC
and the like. Preferably, the selected vector of the present invention has the capacity to autonomously replicate in the selected host cell. Useful prokaryotic hosts include bacteria such as E. coli, Flavobacterium heparinum, R~rcj~ , Streptomyces, Pseudomonas, Salmonella, Serratia, and the like.
To express the snhst~nti~lly pure polysaccharide Iyases of the invention in a prokaryotic cell, it is n~cess~ry to operably join the substantially pure polysaccharide Iyases of the invention CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 sequence to a functional prokaryotic promoter. Such promoters may be either constitutive or, more preferably, regulatable (i.e., inducible or dt,~les~ible). Examples of constitutive - promoters include the int promoter of bacteriophage ~, the bla promoter of the ~ ct~m~ç gene sequence of pBR322, and the CAT promoter of the chloramphenicol acetyl transferase gene 5 sequence of pPR325, and the like. Examples of inducible prokaryotic promoters include the major right and left promoters of bacteriophage ~ (PL and PR)~ the trp, recA, lacZ, lacI, and gal promoters of E. coli, the o~-amylase (Ulmanen et al., J. Bacteriol. 162:176-182 (1985)) and the ~-28-specific promoters of B. subtilis (Gilman et al., Gene sequence 32:11-20 (1984)), the promoters of the bacteriophages of Bacillus (Gryczan, In: The Molecular Biology of the Bacilli, o Ac~ mic Press, Inc., NY (1982)), and Streptomyces promoters (Ward et al., Mol. Gen. Genet.
203:468-478 (1986)).
Prokaryotic promoters are reviewed by Glick (J. Ind. Microbiol. 1 :277-282 (1987));
Cenatiempo (Biochimie 68:505-516 (1986)), and Gottç~m~n ~nn. Rev. Genet. 18:415-442 (1984)).
Proper expression in a prokaryotic cell also requires the presence of a ribosome binding site u~ e~ll of the encoding sequence. Such ribosome binding sites are disclosed, for example, by Gold et al. (Ann. Rev. Microbiol. 35:365-404 (1981)).
Because prokaryotic cells will not produce the substantially pure polysaccharide lyases of the invention with normal eukaryotic glycosylation, expression of the substantial~y pure polysaccharide lyases of the invention of the invention by eukaryotic hosts is possible when glysoylation is desired. Preferred eukaryotic hosts include, for example, yeast, fungi, insect cells, and m~mm~ n cells, either in vivo or in tissue culture. ~mm~ n cells which may be useful as hosts include HeLa cells, cells of fibroblast origin such as VERO or CHO-Kl, or cells of lymphoid origin, such as the hybridoma SP2/0-AG14 or the myeloma P3x63Sg8, and their derivatives. Preferred m~mm~ n host cells include SP2/0 and J558L, as well as neuroblastoma cell lines such as IMR 332 that may provide better capacities for correct post-translational -CA 0223~223 l998-04-29 procec~ing Embryonic cells and mature cells of a transplantable organ also are useful according to some aspects of the invention.
In addition, plant cells are also available as hosts, and control sequences compatible with plant cells are available, such as the nopaline synthase promoter and polyadenylation signal sequences.
Another plc;r~lled host is an insect cell, for exarnple in Drosophila larvae. Using insect cells as hosts, the Drosophila alcohol dehydrogenase promoter can be used (Rubin, Science 240:1453-1459(1988)). ~Itern~tively, baculovirus vectors can be çngine~red to express large amounts of the substantially pure polysaccharide Iyases of the inventionin insects cells (Jasny, o Science 238:1653(1987); Miller et al., In: Genetic Engineering (1986), Setlow, J.K., et al., eds., Plenum, Vol. 8,pp.277-297).
Any of a series of yeast gene sequence t;~ ion systems may also be utilized which incorporate promoter and t~rmin~tion elements from the genes coding for glycolytic enzymes which are produced in large quantities when the yeast are grown in media rich in glucose.
Known glycolytic gene sequences can also provide very efficient transcriptional control signals.
Yeast provide substantial advantages in that they can also carry out post-translational peptide modifications. A number of recombinant DNA strategies exist which utilize strong promoter sequences and high copy number pl~miclc which can be utilized for production of the desired proteins in yeast. Yeast recognize leader sequences on cloned m~nnmz~ n gene sequence products and secrete peptides bearing leader sequences (i.e., pre-peptides).
A wide variety of transcriptional and translational regulatory sequences may be employed, depending upon the nature of the host. The transcriptional and translational regulatory signals may be derived from viral sources, such as adenovirus, bovine papilloma virus, simian virus, or the like, where the regulatory signals are associated with a particular gene sequence which has a high level of ~ es~ion. Alternatively, promoters from m~mms~ n expression products, such as actin, collagen, myosin, and the like, may be employed. Transcriptional initiation regulatory signals may be selected which allow for repression or activation, so that CA 0223~223 l998-04-29 expression of the gene sequences can be mod~ te-l Of interest are regulatory signals which are temperature-sensitive so that by varying the temperature, expression can be repressed or initi~te-1 - or which are subject to chemical (such as metabolite) regulation.
As fli~cn~se~l above, expression of the substantially pure polysaccharide lyases of the invention in eukaryotic hosts requires the use of eukaryotic regulatory regions. Such regions will, in general, include a promoter region sufficient to direct the initiation of RNA synthesis.
Preferred eukaryotic promoters include, for example, the promoter of the mouse metallothionein I
gene sequence (Hamer et al., J. Mol. AppL Gen. 1 :273-288 (1982)); the TK promoter of Herpes virus (McKnight, Cell 31 :355-365 (1982)); the SV40 early promoter (Benoist et al., Nature o (London) 290:304-310 (1981)), the yeast gal4 gene sequence promoter (Johnston et al., Proc.
Natl. Acad Sci. (USA) 79:6971 -6975 (1982); Silver et al., Proc. Natl. Acad. Sci. (USA) 81 :5951-sgss (1984))-As is widely known, translation of eukarvotic mRNA is initi;lt~d at the codon which encodes the first methionine. For this reason, it is preferable to ensure that the linkage between a eukaryotic promoter and a DNA sequence which encodes the substantially pure polyss~h~ri~le lyases of the invention does not contain any intervening codons which are capable of encoding a methionine (i.e., AUG). The presence of such codons results either in a formation of a fusion protein (if the AUG codon is in the same reading frame as the substantially pure polysaccharide lyases of the invention coding sequence) or a frame-shift mutation (if the AUG codon is not in the same reading frame as the substantially pure polysaccharide lyases of the invention coding sequence).
In one embodiment, a vector is employed which is capable of integrating the desired gene sequences into the host cell chromosome. Cells which have stably integrated the introduced DNA into their chromosomes can be selected by also introducing one or more markers which allow for selection of host cells which contain the expression vector. The marker may, for example, provide for prototrophy to an auxotrophic host or may confer biocide resi~t~nce to, e.g., - antibiotics, heavy metals, or the like. The selectable marker gene sequence can either be directly CA 0223~223 1998-04-29 linked to the DNA gene sequences to be expressed, or introduced into the same cell by co-transfection. Additional elements may also be needed for optimal synthesis of the substantially pure polysaccharide lyases of the invention mRNA. These elements may include splice signals, as well as transcription promoters, enhancers, and t~rmin~tion signals. cDNA ~ ;s~ion vectors s incorporating such elements include those described by Okayama, Molec. Cell. Biol. 3 :280 (1983).
In a preferred embodiment, the introduced sequence will be incorporated into a plasmid or viral vector capable of autonomous replication in the recipient host. Any of a wide variety of vectors may be employed for this purpose. Factors of hllpol ~Ice in selecting a particular 10 -plasmid or viral vector include: the ease with which recipient cells that contain the vector may be recognized and selected from those recipient cells which do not contain the vector, the number of copies of the vector which are desired in a particular host; and whether it is desirable to be able to "shuttle" the vector between host cells of diLrel~l,l species. Preferred prokaryotic vectors include plasmids such as those capable of replication in E. coli (such as, for example, pBR322, ColEl, 15 ~ pSC101, pACYC 184, and 7~VX. Such pl~mi~1~ are, for example, disclosed by Sambrook, et al.
(Molecular Cloning: ~ Laboratory Manual, second edition, edited by Sarnbrook, Fritsch, &
ni~ti~, Cold Spring Harbor Laboratory, 1989)). P~aci~1u~ pl~cmitl~ include pC194, pC221, pT127, and the like. Such plasmids are disclosed by Gryczan (In: The Molecular Biology of fhe Bacilli, Academic Press, NY (1982), pp. 307-329). Suitable Streptomyces plasmids include 20 pIJ101 (Kendall et al., J. Bacteriol. 169:4177-4183 (1987)), and streptomyces bacteriophages such as ~C31 (Chater et al., In: Sixth International Symposium on ~ctinomycetales Biology, ~k~ mi~i Kaido, Budapest, Hungary (1986), pp. 45-54). Pseudomonas plasmids are reviewed by John et al. (Rev. Infect. Dis. 8:693-704 (1986)), and Izaki (Jpn. J. Bacteriol. 33:729-742 (1978)).
pl~r~ d eukaryotic plasmids include, for example, BPV, EBV, SV40, 2-micron circle, and the like, or their derivatives. Such plasmids are well known in the art (Botstein et al., Miami Wntr. Symp. 19:265-274 (1982); Broach, In: The Molecular Biology of the Yeast Saccharomyces:

CA 0223~223 1998-04-29 W O 97/165~6 PCTAJS96/17310 Life Cycle and Inheritance, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, p. 445-470 (1981); Broach, Cell 28:203-204 (1982); Bollon et al., J. Clin. Hematol. Oncol. 10:39-48 (1980);
~ni~fi~, In: Cell Biology: A Comprehensive Treatise, Vol. 3, Gene Sequence Expression, ~c~-lemic Press, NY, pp. 563-608 (1980)). Other ~l~r~lled eukaryotic vectors are viral vectors.
For example, and not by way of limitation, the pox virus, herpes virus, adenovirus and various retroviruses may be employed. The viral vectors may include either DNA or RNA viruses to cause expression of the insert DNA or insert RNA. In addition, DNA or RNA encoding the substantially pure polysaccharide lyases of the invention polypeptides may be directly injected into cells or may be impelled through cell membranes after being adhered to microparticles (see below).
Once the vector or DNA sequence co~ .g the construct(s) has been prepared for sion, the DNA construct(s) may be inkoduced into an apl)lol,liate host cell by any of a variety of suitable means, i.e., transformation, transfection, conjugation, protoplast fusion, ele~;L.oE,ol~lion, calcium phosphate-precipitation, direct microinjection, and the like. After the introduction of the vector, recipient cells are grown in a selective medium, which selects for the growth of vector-co,~i ~; . .; .-~ cells. Expression of the cloned gene sequence(s) results in the production of the substantially pure polysaccharide lyases of the invention. This can take place in the transformed cells as such, or following the induction of these cells to dirrel~llliate (for example, by zl~lmini~tration of bromodeoxyuracil to neuroblastoma cells or the like).
The foregoing written specification is to be considered to be sufficient to enable one skilled in the art to practice the invention. The present invention is not to be limited in scope by the particular examples disclosed herein as these embo-liment~ are intencle~l only as illustrations of the aspects of the invention and any recombinant polysaccharide lyases that are functionally equivalent are within the scope of the invention. Therefore, any sequences that are functionally equivalent of those described herein are within the spirit and scope of the claims appended hereto. Indeed, various modifications of the invention in addition to those shown and described herein will become ~ l to those skilled in the art from the foregoing description.

CA 0223~223 l998-04-29 W O 97/16556 PCT~US96117310 Examlple 1 pl~rification of hf~2~rins~e I: Lyophilizedpowdered extracts of F. h~c~,.lilll.,.~ were prepared according to the method of Yang et al. (1985). Partially purified heparinase I was ~I~. d by step gradient elution of powdered cell exkacts from a hydroxyapatite column followed by reverse adsorption on a QAE-Sephadex colurnn. Further p~lrific~tion of the enzyme was accomplished with a chromatofocusing, 1 cm x 18 cm column with PBE resin (Pharmacia).
A 1.5-2.5 ml aliquot of protein (0.5-1.5 mg) in 0.01 M phosphate (pH 6.8) was applied to the colurnn equilibrated with 0.025 M ethanolamine (pH 9.4 with acetic acid). Elution was carried out with 150 ml of 10% Polybuffer 96 (pH 6.0 with acetic acid). The chromatofocused o h~p~rin~e I eluted between 10 and 15 ml (pH 8.0-8.2). Fractions (1.5-2.0 ml) were collected in tubes co~l;.;~.;.,p~ 0.2 ml of 0.5 M phosphate buffer at pH 6.8. Immediately after collection, the fractions were assayed for heparinase I activity. Prior activity d~lf l . l, ~ tion in the presence of Polybuffer showed no inhibition or i~ relc;llce by the ampholytes. The active fractions were pooled, and NaCl was added from a 2.0 M aqueous solution to give a final concenkation of 0.1 M. Heparinase I was concentrated and equilibrated with a buffer con~i~tin~ of 0.01 M NaH2PO4 and 0.1 M NaCl at pH 6.8 (PBS) with Centricon P-30 microconcentrators (Amicon, MA). The recovery of activity from the column was up to 90%. The resulting enzyme, equilibrated with PBS, is stable for up to 5 days at 4~C.
Hepar~nase I was purified to homogeneity by reverse-phase high pressure liquid chromatography with an HP 1090 (equipped with a diode array detector for multiple wavelengths, an on-line chart recorder monitoring 210 and 277 nm wavelengths) on a Vydac C,8 reverse-phase column. The enzyme was eluted with a gradient of 0 to 80% acetonitrile in 0.1%
TFA for 120 min. Heparinase I appeared as a doublet. Both the major and minor peaks had similar W and tryptic digest profiles (S~ kh~ran, 1991). The major peak was usedthroughout this work. It is believed that the isoforms of h~dlhlase I are due to some unknown post-tr~n.clational modification (Zimmermarm, 1989). However, the labeling results were unaffected for samples in which the two peaks were not clearly resolved (Sasisekharan, 1991).

CA 0223~223 1998-04-29 W O 97/16556 PCTnJS96/17310 The enzyme was inactive following reverse phase HPLC. Protein concentrations were etermined using Micro BCA reagent (Pierce Inc., IL) relative to a bovine serum albumin standard. To t1~termine the purity and homogeneity of heparinase I, mass spectrometry was performed on a Laser MAT (Finni~n, CA) (S~ çl~h~ran et al., 1994). Amino acid composition 5 analysis was performed on an amino acid analyzer (Model 420, Applied Biosystems, CA) in Biopolymers Laboratory, Center for Cancer Research, MIT.
Heparinase was radio-iodinated with the Enzymobead reagent (BioRad), followed byremoval of unbound [l25I] by passage over a PD-l 0 column (Pharmacia) equilibrated with the a~ vL)l;ate buffer. The radio-labeled enzyme was diluted with unlabeled enzyme. The specific lO activity of the protein ranged 104-105 cpm/mg.

le 2 Pylidylet~ylation of cysteines: Pyridylethylation is a cysteine modification method that aLkylates the cysteine using 4-vinyl pyridine (4-VP) (Andrews & Dixon, 1987). The alkylating 15 group, 4-VP, is a hydrophobic residue that is stable in modified cysteines. The 4-VP modified cysteine(s) can be characterized easily by amino acid analysis. In this work the amino acid analyses on the 4-VP cysteine heparinase I indicated the presence of 2.14 _ 0.2 cysteines. There was no increase in pyridylethyl cysteine content following treatment with DTT demonstrating the absence of any disulfide bonds.

~y~ple 3 Radio-labelin~ and tryptic mapp;n~ of he~a~ ase I: Heparinase I which had been treated with 2 mM [3H]iodoacetic acid in the presence of gll~ni~line hydrochloride and DTT had ~ 0.55 +
0.05 X 104 cpm [3H]iodoacetic acid/~lg of heparinase or 2.2 _ 0.05 x 105 cpm [3H]iodoacetic 25 acid/nmole of heparinase. Physical mapping of the cysteines of heparinase I was performed by peptide mapping with trypsin, followed by amino acid sequencing. The [3H] labeled peptides CA 0223~223 1998-04-29 were peak 7 or Cysl35, peak 65 or Cys297, and a third peak: peptide 61 which also turned out to be Cys297. The sequences of the three peptides corresponding to these peaks were:
Peak7 KGIC*EQGSSR
Peak65 KMPFAQFPKDI C* WITFDVAIDWTK
Peak61 KDIC*WITFDVAIDWTK

The above results show that mature heparinase I from F. h~l,~;.,l.,,, contains two free cysteines and not a disulfide bridge.

F~ le 4 Modification with Or~nomercurials: The reversible, sulfhydryl specific anion, PCMB, was utilized to determine the effects of sulfhydryl modification on heparinase I activity.
Chromatofocused hepali"ase I treated with PCMB at 2.5-100 ~lM and 4~C resulted in a reversible loss of 95 ~ 5% of enzyme activity. Upon addition of 10 mM DTT, up to 90% of the lost 15 enzyme activity is recovered within 1 h at 4~C, verifying the sulfhydryl specificity of the reaction. Overnight incubations did not result in further inactivation of the enzyme, and 90% of the activity was recovered subsequently by tre~tment with 10 mM DTT. The time course of inactivation in the presence and absence of heparin also was deterrnined. In the presence of 0.5 mg/ml heparin (~5 x K",), the rate of inactivation was significantly decreased. Rate constants 20 were det~rminP-l by assuming pseudo first order kinetics and fitting of the data to the equation:

At = Ao exp (-t/~) + A., where At is the fractional activity at time t, Ao is the initial fractional activity, A_ is the residual 25 activity at infinite time, and c is the inactivation time constant in minl-tes or the reciprocal rate constant. Time constants were obtained by a nonlinear least squares fit of the data to the equation. The best fit parameters obtained in the absence of heparin were Ao = 0.72 ~ 0.05, A_ = -CA 0223~223 1998-04-29 W O 97/16556 PCTrUS96/17310 0.25 _ 0.03, and ~ = 0.8 + 0.1 min. In the presence of 0.5 mg/ml heparin, the best fit parameters were Ao = 0.67 ~ 0.08, A~ = 0.28~t 0.03, and c = 5 + 1 min. The corresponding rate con~la~
with 0.0 and 0.5 mg/ml heparin are 1.2 min l and 0.2 min I, respectively. Thus the presence of heparin reduces the inactivation rate 6-fold. The heparin concentration in the assay medium (25 mg/ml) was much larger than the K,l, of 0.1 mg/ml (Yang et al., 1985); consequently, any additional heparin introduced did not alter the kinetics.
The use of PCMB-sulfonic acid resulted in similar inactivation behavior. PCMBS
treatrnent was carried out following reduction with DTT in order to ascertain whether the modifications of any exposed sulfhydryls affected the activity. HeparinaseI pretreated with 1 o mM DTT for 4 h at 4~C under nitrogen followed by modification with 2.5 mM PCMBS resulted in the same reaction kinetics as observed with untreated heparinase. Heparin was not included in these experiments. Further, similar heparinase inactivation results were obtained when recombinant heparinase I was used in the PCMB labeling studies.

F.~ ple 5 N-etl~ylmaleimide Derivslti7~tion: Different sulfhydryl reagents often exhibit disparate reactivities with proteins due to protein structural properties (Vallee & Riordan, 1969). The effect of NEM modification on hep~rin~e I activity was examined in an attempt to elucidate structural influences on the cysteine reactivities. Tre~t~nent of heparinase I with 1 mM NEM at pH 7.0, showed little change in activity over an 8 h period. Heparinase I treated with 1 mM NEM
overnight at 4~C, result in an activity loss of about 15%. In contrast, in the presence of 10 mM
NEM pH 7.0 at 4~C, 15% of the en7ymatic activity was lost within 45 min.
In order to ascertain whether significant levels of NEM bind heparinase I, labeling studies with [3H]NEM were undertaken. Non-denatured heparinase incubated with 1 mM [3H]NEM for 8 h incorporates 0.3 x 10-9 nmole [3H]NEM/~g heparinase I, as det~rmine-1 from radio-labeled heparinase I electroeluted from an SDS gel. If the reaction was allowed to proceed for 20 h, up - to 1 x 10-9 nmole [3H]NEM/llg heparinase I was incorporated with a corresponding 15% loss of CA 0223~223 1998-04-29 W O 97~16556 PCTAUS96/17310 activity. In conkast, if the enzyme was first denatured by incubation with either 0.1% SDS or 5 M guanidine hydrochloride, about 6 x 10-9 nmole [3H]NEM/~g heparinase I was incorporated within an 8 h incubation at 4~C.

~,y7~nlple 6 nerivatizatioIl by Iodoacet~mide and Iodoacetic Acid: The effect of reagent charge on cysteine reactivity was investig~te~l by use of the negatively charged reagent iodoacetic acid and its neutral analogue, ioclo~cet~mide. In addition to their charge difference, the reactivity of io~10~qccetz-micle is 5-7 times faster than iodoacetic acid with free cysteine in aqueous media o (MacQuarrie & Bernhard, 1971).
Heparinase I incubated with 2, 5, 10, and 120 mM iodc S~et~mide in PBS at pH 7.0 and 4~C for up to 24 h exhibited little change in activity. A 15% inactivation occurred only after a 24 h incubation in the presence of 120 mM iodoacetamide. Iodo~cet~mide, therefore, does not significantly modify heparinase I.
In contrast, in the presence of 2 mM iodoacetic acid in PBS at 4~C, 95 ~ 5% of heparinase I was inactivated within 10 min. The inactivation rate was concentration dependent: at 1 mM and 0.1 mM iodoacetic acid, inactivation was complete within 15 min and 15 h, respectively. The sensitivity of the iodoacetic acid binding site to the presence of heparin was demonstrated by the decrease in the inactivation rate in 500 mM iodoacetic acid from 3 ~t 1 x 10-3 h-l to 5 ~ 2 x 10-4h-20 1 in the presence of 2 mg/ml heparin. The retention of activity relative to untreated heparinase I
was 15 ~ 5%. Pretreatment of the C.I~-ylllC for 4 h at 4~C with DTT under nitrogen had no effect on the modification.
It is known that the iodoacetic acid reactive form of cysteine is the mercaptide anion, and that the reaction rate increases with increasing pH (Torchinsky, 1981). In particular, the relative 25 -free cysteine alkylation rates at pH 5.6, pH 7.02, and pEI 8.36 are 0.14, 1.0, and 2.1, respectively (Torchinsky, 1981). If the heparinase I cysteine were unaffected by the presence of nearby amino acids in the protein, the iodoacetic acid inactivation rates at 6.5 and 8.0 would be expected to CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 vary by an order of m~gnitllf1ç. The pseudo first order heparinase I inactivation rate co~
obtained at pH 6.5, 7.0, 7.5, 8.0 and 8.5, however, varied very little over the pH range. The rate - con~ , k, were determined from the activity after a determined time, A" the initial activity Ao~
the residual activity at inf nite time, Ao~ and the equation:

k = (l/c) ln [(At - AO~)/Ao]

The small variation in the rate of inactivation suggests that the cysteine was activated by the presence of nearby basic amino acids (Hammond & Gutfreund, 1959, Rabin & Watts, 1960).
o The above results, i.e the marginal modification of heparinase I by iodoacet~mi~le and the significant inactivation of heparinase I by iodoacetic acid, corroborates with the hypothesis that the environment around the cysteine residue is basic.

ple 7 Salt dependence of PCMB labelin.~: In order to show that the positive environrnent around the PCMB-reactive cysteine influences the labeling of the negatively charged PCMB, cysteine labeling by PCMB was performed under different salt concenkations and the time course of inactivation of heparinase I by PCMB with increasing salt concentrations was calculated. Heparinase I inactivation rate by PCMB was si~2nific~ntly reduced with increasing salt concentration 50, 100 and 200 mM NaC1. Indeed, no inactivation was detectable at a salt concentration of 200 mM NaCl. This result is consistent with the observation that the environment around the cysteine is positively charged, and the alteration of the electrostatic properties of this region by ch~nging the salt concentration has a significant effect on the rate of the PCMB based inactivation of the thiol group. Thus, this result supports the conclusion that the t;llvho~ lent around the PCMB-reactive cysteine is basic.

~ple 8 CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 Mappin~ the Mo-lified Cysteine: In order to further verify that the PCMB-reactive cysteine was at the same site as the iodoacetic acid binding cysteine, [3H]iodoacetic acid was reacted with non-len~tllred PCMB-modified heparinase I, and the amount of label incorporated was compared to that of non~len~t~-red, untreated heparinase I labeled with [3H]iodoacetic acid 5 under identical conditions. In these experiment~, it was found that the [3H]io-lo~eetic acid labeling was reduced by 80% following tre~tment with PCMB. This suggested that the iodoacetic acid binding site and the PCMB binding site are identical. This was conclusively (letcrmine<l by peptide mapping by trypsin digestion and amino acid sequencing of the modified h~ e I
cysteine.
The PCMB-labeled heparinase I was isolated, denatured and then reacted with iodoacetamide to block the other cysteine. Following this, the enzyme was treated with DTT to remove the bound PCMB, and then labeled with [3H]iodoacetic acid. Modified hep~rin~ee I was digested with trypsin and the tryptic peptides were separated. Only one cysteine, Cysl35, was selectively labeled by [3H]iodoacetic acid. Cys297 was not labeled by [3H]ioclo~cetic acid in this 15 . experiment. In another ~x~e~ lent, heparinase I was first labeled at the reactive cysteine with PCMB. The enzyme was then denatured, labeled with [3H]iodoacetic acid, and re-chromatographed to remove the excess radiolabel. Following this, the enzyme was digested with trypsin and the tryptic peptides were separated by RP-HPLC. In this experiment Cys297 was selectively [3H] labeled, while Cysl35 was not. The results ofthe above e~e~ ents taken 2C\ together, confirm that Cysl35 is the PCMB-labeled or the active site cysteine. In addition, [3H]iodoacetic acid labeling had little or no cross-reactivity and was selective in labeling the cysteines.
F~ ple 9 Cysteine-~o-lified Recomb;n~nt Heparinase: Site-directed mutations were performed to 25 confirm the role of Cysl35 in hepz~rin~ee I activity. Seven mutant recombinant heparinases were rle~i~ne~l C135S (Cysl35 to serine conversion), C135H (Cysl35 to hi~ti~line conversion), C135E
(Cysl35 to gl--t~m~te collvelsion), C135D (Cysl35 to aspartate conversion), C135A (Cysl35 to CA 0223~223 1998-04-29 W O 97/16556 PCTnJS96/17310 alar~ine conversion), C297S (Cys297 to serine conversion), and C297A (Cys297 to alanine converslon).
Recombinant polysaccharide Iyases were produced as soluble protein in BL21DE3 E coli host, using the pET 15b system, where c~x~l~ssion is driven by bacteriophage T7 Polymerase.
5 This construct has a hieticline tag (6 consecutive histidines), which c- n~titlltes a high affinity site for Ni2+, and a thrombin cleavage site in a 21 amino acid N-t~orminz~l leader sequence. The ~x~l~,3sion is in~luce~l by IPTG (isopropyl-~-D-thiogalactoside). The -L hep~rin~ce construct starts with a sequence which reads Met, Gln22, Gln23, Lys24, Lys25, Ser26 .... (~ h~r~n et al., 1993). The Met residue was added before the Gln22 to introduce a start codon. The Cysl 35 and Cys297 mutations were introduced as part of PCR primers. These primers, together with the T7 promotor (5') and T7 terminator (3') primers (Novogen, WI) (which flank the hep~rin~e gene), were used to create two PCR products that overlap in sequence, with the -L hep~rin~e gene construct as a template. The overlapping products were isolated from low melt agarose (SeaPlaque, FMC, or GIBCO BRL, Gaithcl~,bL~g, MD), denatured (100~C), and allowed to 15 reanneal (room temperature) to produce two possible heteroduplex products (Higuchi, 1990).
The heteroduplex with the recessed 3' ends was filled-in using ~ polymerase. This fr~gment was used as a template in a 12 cycle PCR (Higuchi, 1990) with the 5' and the 3' primers ~,~.e~ ely. The PCR product was isolated from a low melt gel and ligated overnight directly into T-vectors (Marchuk, et al., 1991). T-vector was prepared as described in Marchuk et al., 20 1991. Briefly, pBluescript (Stratagene, LaJolla, CA) was digested with EcoRV (New F.n~l~n~l Biolabs, Beverly, MA) and isolated and gel purified from a low melt gel. The purified linear plasmid was then incubated with ~ polymerase (lunit/~Lg plasmid/20 ~11 volume) (Perkin Elmer, Norwalk, CT) and 2mM dTTP for 2 hrs at 70~C, using standard buffer conditions. The sub-cloned heparinase I PCR fragments were excised from T-vector by digestion with ~I and 25 ~EnHI, gel purified, and then ligated into pET-15b plasmid (predigested at the NdeI and ~mHI
sites and gel purified) using T4 DNA ligase (New F.n~l~ncl Biolabs, MA). The ligation ~ Lult;
then was used to transform DHSo~ competent cells (GIBCO BRL). The plasmid c~ ;"il-~ the CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 recombinant Iyase gene in pET-lSb was isolated, purifled using Miniprep (Qiagen, Charsworth, CA), and used to transform the host cell BL21(DE3) (Novogen, WI). Recombinant hep~rin~ee I
construct devoid of the putative signal sequence (-L r-heparinase I) was also expressed as a control (Sasisekharan et al., 1993).
= The constructs were transformed in BL21(DE3) (Novagen), grown overnight, diluted in 100 ml LB, 250 ~lg/ml ampicillin and grown to an OD60o of 0.5. The culture was in~ ed with 1 mM IPTG for 2 hours, harvested by centrifugation (4~C, 3500g x 10 min), washed in cold phosphate buffered saline (PBS) and resuspended in 1/20th volume binding buffer (20 mM Tris, 500 mM NaCl, 5 mM rmic~7c 1e). The resuspended culture was placed in an ice bath, sonicated for 2 min using a Branson 450 sonicator (Branson, Danbury, CT) (power 3, 50% pulse) and centrifuged at 4~C and 15,000 g for 30 min. The s~ t~ was assayed for activity and purified by Ni2+ affinity chromatography using sepharose 6B Fast Flow resin covalently linked to nitrilotris~f~etic acid (Novogen, WI). Briefly, the resin was charged with S column volumes 200 mM NiSO4and equilibrated with 5 colurnn volumes binding buffer. Then, 6-10 ml sample was applied followed by 12 ml binding buffer, 9 ml 15% elution buffer (20 mM Tris, 500 mM NaCI, 200 mM Imidazole) and 10 ml 100% elution buffer. The enzymes were recovered in 4 ml of the 100% elution step, .l~lt~d on two PD10 colurnns (BioRad, Richmond, CA) and incubated overnight at 4~C with 0.5 ur~its thrombin (Novagen, WI). Cleaved enzymes were applied to the stripped (20 mM Tris, 500 mM NaCI, 100 mM EDTA) and regenerated column and collected in the flow through fraction. SDS-PAGE (Laemmli, 1970) was carried out using precast 12% gels and a Mini Protean II a~ dld~Lls, and stained with the Silver Stain Plus kit.
The level of protein expression for all the recombinant heparinases was identical in the BL21(DE3) host. While -L r-heparinase I control was expressed as a soluble protein in E. coli with an activity of~ 5.2 U/mg of ~. cQli crude extract (~ ekh~ran et al., 1993), the C135A r-heparinase I was expressed in BL21(DE3) with no enzymatic activity. Interestingly, the C135S
r-hep~rin~ce I was expressed in BL21 ~DE3) with an activity of ~ 0.06 U/mg of E. cQli crude extract. The C135H, C135E, and C135D recombinants show~50% ofthe activity ofthe -L r--CA 0223~223 1998-04-29 heparinase. Impol L~ y~ the mutations at Cys297 (C297S and C297A) were both expressed in the same host with no change in their enzymatic activity compared to the -L r-heparinase I
control.
The r-heparinase degradation of heparin was identical to that of the purified F. h~a- illWll s heparinase I, producing the two di-, the three tetra-, and the hexasaccharides. The above results taken together show that Cysl35 is important for heparinase I activity and that altering Cys297 did not alter heparinase I activity.

Example 10 Calcium Dependence of Heparinase I Activity: Heparinase I samples were extensively desalted using Centricon P-30 microconcentrator to remove residual calcium from the hydroxylapatite step during the enzyme purification (Yang, et al., 1985; Sasisekharan et al., 1994). The heparin concentration was fixed at 25 mg/ml in all t;x~ ent~, and only the calcium concentration was varied. Activity was seen to increase with calcium concentrations increasing up to about 5-10 mM. A region of heparinase I (residues 206-213) was found to be homologous to the calcium binding loop of the EF-hand structural domain (Kretsinger et al., 1991). Of the five amino acids that are involved in coor ~in~ting calcium, four are conserved in heparinase I
(Table II). Also the glycine and hydrophobic residue at the top of the loop are conserved. This suggested a calcium coo~ in~ site in heparinase I.

F,Y~nUPIC11 Heparin Afflnity Chromato~raphy: The affinity separation of heparinase I was carried out in the presence and absence of calcium. Heparinase I was seen to bind to heparin-POROS, and the bound enzyme could be eluted at a salt concentration of about 200 mM. The protein eluted as 2S a doublet, con~i~tt-n1 with results from heparinase I purification (Sasisekharan, et al., 1993).
When the affinity separation was carried out in the presence of calcium (5mM), hep~rin~e I

CA 0223~223 1998-04-29 eluted in the void volume since the enzyme cleaves the heparin to which it binds (this was conrllllled by the appearance of oligosaccharide products in the void volume).

~Ys~nlple 12 Affinitv Co-electrophoresis: Affinity co-electrophoresis (ACE) was used to 4u~lLiry heparin binding to heparinase I. The technique measures the extent of binding based on the retardation of heparin when electrophoresed in the presence of hepslrinz-ce I embedded in an agarose gel. ACE was carried out in the presence or absence of iodoacetic acid to rietennine the irnportance of the active site Cysl35 in the binding of heparin to heparinase I and in the absence of calcium to prevent heparin degradation. At a sufficiently high enzyme conct;llLl~Lion, the migration of heparin is retarded in a dose-dependent manner. There is no dirr~,le.llce in the retardation of heparin for the iodoacetic acid modified heparinase I when col~lp~t;;d to the unmodified heparinase I. This result indicates that blocking the active site cysteine does not alter heparin binding.
To rlett~rrnine a binding constant, a Scatchard plot was obtained by plotting R/C vs. R, where R is the retardation coefficient R= (Mo -M)/Mo, Mo is the mobility of free heparin, and M
is the observed heparin mobility in a zone with protein concentration of C. ~llming a single site, bimolecular association, the data were fitted to a straight line with a slope of -l/Kd (Lee and Lander, l 99 l ). The dissociation c~)n~ for heparinase-heparin binding was found to be 60 nM
by this technique. Furthermore, an ACE gel of heparin-heparinase carried out in the presence of calcium showed extensive smearing of the heparin band, since heparinase I cleaved heparin in the presence of calciu}n. No heparin retardation could be observed on this gel.

E~mple 13 Heparin Blottin~ of CnBr Di~ests of Heparinase I: CnBr digested hep~rin~ee I s~dldl~d by SDS-PAGE resulted in lO peptide fragments. Heparinase I contains S intl rn~l methionine residues (CnBr sites) two of which are adjacent, so for complete digestion, only 5 fr~gments CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310~ -39-should be expected. Only 4 of the smaller peptides could be sequenced as the larger fr~gmente,based on molecular weights and sequencing, probably represented partial digests from the N-terminus which previously was shown to be blocked (~eie~1~h~ran~ et al., 1993). The CnBr digested heparinase I fr~gmente were transferred onto nitrocellulose and hybridized with labeled 5 heparin, and counted for l25I incorporation. The binding of l25I-heparin to one peptide band (CnBr-8), was 2-4 times as high as binding to the other bands and to controls. Similar results were obtained by an alternative method where the peptide bands were cut out and then hybridized individually. CnBr-8 is a partial digest of approximately 10 kDa, ~ hlg amino acids 196 to a~ o~hllately 290 of the heparinase I primary sequence. It has a lysine rich N-terminal region, 10 c- nt~ininP two Cardin-Weintraub heparin binding consensus sequence and a calcium binding loop ofthe EF-hand structural domain. CnBr-7 is ~13-kDa, spanning amino acids 272 to a~ hllately 360. The region from 272 to 290 is common to CnBr-7 and CnBr-8 and, since CnBr-7 did not bind heparin, it is thus excluded from being a part of the heparin binding domain.
These results indicates the region 195-270 contains the primary heparin binding site and that this 15 site is still functional in the isolated CnBr-8 peptide. To further narrow down the heparin-binding region, we performed tryptic digests which cleave heparinase I to much smaller fragments than CnBr.

F,~?le 14 20 Coml~etitive B;nc1in~ and Dot-blots with Tr,vptic Di~ests of Heparinase I: Tryptic mapping of hepzlrin~ee I has been standardized using RP-HPLC (~ei.eçkh~ran, et al., 1993). Even though hep~rin~ee I is a very basic protein (having a pI of 9.1), it binds very well to a hydrophobic surface as its elutes at a relatively high acetonitrile concentration of 72% in RP-HPLC.
Interestingly, we found that heparin, but not chondroitin sulfate, was able to prevent heparinase I
25 binding to a reverse-phase column in a concentration dependent manner.
We tested the ability of heparin in protecting the heparin binding domain of hep~rin~ee I
from trypsin cleavage. Under the conditions tested, we observed that heparin was ineffective in CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 -40- _ protecting the heparin binding domain but, nonetheless, it was able to specifically compete with the binding of some hepz~rin~ee I tryptic peptides to the reverse phase colurnn. Peaks that shifted significantly in their elution time, or disappeared (presumably eluting in the void volume), represent tryptic peptides that binds to heparin. Chondroitin sulfate was used as a control to 5 account for non-specific ionic effects of heparin on elution of the peptides. Compared to a control tryptic map, no significant changes were observed in the tryptic digests performed in the presence of increasing concentration of chondroitin sulfate except for the appearance of a peak about 42 min and the overall ~limini~hing of peak sizes for td9, those eluting between 52-58 mins, and tdS0. However, in the presence of increasing concentrations of heparin, the following peaks were altered reproducibly: td4, td9, peaks eluting between 52-58 mins td39, td 45, td S0. As the peptides td9, those eluting in the region between 52-58 mins, and tdS0 were altered by both heparin and chondroitin sulfate, it is probable that these peptides non-specifically interact with these acidic polysaccharides. However, in the presence of heparin alone (or heparin with chondroitin sulfate) td4, td39 and td45 were absent (from the region where they should elute) in the tryptic map, indicating specific binding to heparin. In a dot blot assay, for specific binding of i2SI heparin to heparinase I tryptic peptides, in the presence of a 100 fold excess of cold chondroitin sulfate, only td45 showed 125I signal. In addition, there were l25I signals near the isocratic region of the chromatogram where di- and tri-peptides, cont~ining Lys and Arg residues, elute.
The sequences of tryptic peptides from heparinase I are given in Table III. It can be concluded that td45 (residues 215-221) and td4 (residues 132-141) are the only peptides from the tryptic digest experiments that bind specifically to heparin; con~i~tent with td39 being a part of CnBr-8 peptide, and td4 being a part of the active site of heparinase I. The combined heparin binding results from experiment~ with CnBr and tryptic digests of heparinase I points to the region of residues 195-221 as being directly involved in heparin binding. Importantly, the region from 195-220 contain multiple Iysines and is likely to be degraded to very short peptides (di and CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 tripeptides) by trypsin. Thus, it would not have been expected to show up on the tryptic digest chromatogram.

F,~ ple lS
Synthetic Heparin Bindin~ Domain of Heparinase I: The region 196-213 was synthesized as a peptide (HBP-I). The peptide (HBP-I) has a ~4 micromolar binding affinity for heparin dodçl~c~-~charides. Interestingly, HBP-I affected the product profile of hep~rin~ee I degradation of heparin. As mentioned earlier, heparinase depolymerization of heparin results in two disaccharides, three tetrasaccharides (1-3), and a h~ çcharide. In a concentration dependent o manner, the addition of HBP-I to the reaction mixture caused the peak corresponding to tetrasaccharide 3 (/~U2s HNS,6S I2S HNS 6S) to disappear. When tetrasaccharide 3 was isolated and degraded with heparinase I in the presence of HBP-I, a m~rkç-l increase in the amount of disaccharide was observed. A control peptide with similar charge properties (and at the concentration ranges tested above) had no effect on the enzyme activity or on the oligosaccharide product profile. This demonstrates that HBP-I affects the selectivity of heparin degradation by heparinase I: Tetrasaccharide 3, but not tetrasaccharides 1 or 2, is degraded to a large extent in the presence of HBP-I.

~.Y:~ple 16 PCMB Protection ancl Tryptic Di~est: Heparinase I derivitization by sulfhydryl specific reagent PCMB inactivated the enzyme due to selective modification of the active site cysteine or Cysl35 (see above). Further, the inability to selectively label Cysl35 using PCMB in the presence of heparin indicated the existence of a heparin binding site in close proximity to Cysl 35. To test this hypot_esis, tryptic digestion of PCMB modified heparinase I (PCMB-heparinase I) was carried out to determine if PCMB was able to protect the heparin binding sequence from trypsin cleavage. The PCMB-heparinase I tryptic map was marked by the appearance of a new peak. The peptide corresponding to this new peak consisted of residues CA 0223~223 1998-04-29 wo 97/16556 PCT/US96/17310 200-209 of heparinase I. This result suggests that PCMB labeled Cysl35 protects this lysine-rich peptide (the heparin binding sequence) from trypsin cleavage, when compared to a control digest where this peptide is not observed. This result is consistent with the notion of a heparin binding site in close proximity to the active site Cysl35.

~Ys-~ple 17 B;n-lir~ Dom~7in-~o(lified Recombin~nt Heparinase: To further investigate the function of the heparin/calcium binding domain, a series o~ recombinant lyases were produced in which the binding domain was modified by site-directed mutagenesis. The recombinants were 10 produced by the same method described above for cysteine ml~t~nte For example, a mutant with His203 to alanine conversion (H203A) was constructed and both the mutant and the wild type r-heparinase I were expressed in ~Ç~li. -L r-heparinase I
degradation of hP,p~rin was i(l~ntic~l to that of the purified F. h~ . " heparinase I, producing the two di-, the three tetra-, and the hex~c~cch~rides described above. The H203A mllt~nt, on the other hand was completely inactive. Fetim~tecl from the intensity of the purified bands, the combined yield of protein expression and purification is identical for both wild type and mutant hep~rin~ee This result demonstrates that His203 is critically required for enzyme activity. In addition, the results strongly suggests that the heparin binding region around residue 203 is in close ~ hllily to the scissile bond during catalysis.
As additional examples, recombinant polysaccharide lyases were produced by site-directed mutagenesis in which Lysl98 and Lysl99 were substituted by alanine (K198A, K199D), aspartate (Kl 98D, Kl 99D) and arginine (Kl 98R, Kl 99R). The replacement of the positively charged lysine with the positively charged arginine had no ~par~llt effect on activity or product profile. Replz~l?ment of either lysine with the neutral alanine or negative aspartate resulted in 25 product profiles in which disaccharide 1 and tetrasaccharides 2 and 3 were negligihle and ~1ie?~f h~rjde 1 and tetr~e~c-~h~ricle 2 were reduced to a~lv~hllately 50% of the abundance obtained with native hep~rin~ee I.

- W O 97/16556 PCTrUS96/17310 Other recombinant polysaccharides produced in accordance with the present invention are shown in Table IV along with indications of their kcat values and activity after overnight incubation with heparin. These polysaccharide lyases are illustrative and not exhaustive of those enabled by the present disclosure.

CA 0223~223 1998-04-29 WO 97/16556 PCTnJS96/17310 TABLE I

Turn#PB 1 PB2 PB3 SGNIP VQAD

NKWV VGIN

3 67-70 75-77 LRFN YRF

4 107-110 116-117 120-122 TNDF SV NAQ

5 128-13 1 140-143 146-148 YHYG SRSY SVY

6 154-156 159-160 164-167 PDN TI WEIGA

7 171-175 178-179 181-184 TLVAT GE KTLS

ITYV WKV

TLAFG YFYIK

RNNA NPE

C VVI FDVA

DVMMTY AHIV

W O 97/16556 PCT~US96/17310 -45- _ TABLE II

EF-handhomology n c x x c x c gly x h c x x c n Hep~nn~ee I V206 E K K D K D G K I T Y V A G220 Score + + + + + + +

The table shows the central Ca2+ coor-lin~ting homology domain of EF-hands, with the functional amino acids bolded (Kretsinger, 1975).

"c" indicates the Ca2~ coor iinslting amino acids, D,N,S,T,E or Q.
"h" indicates amino acids with hydrophobic side groups, I, L or V.
"n" indicates nonpolar amino acids, I, L, V, M, F, Y, W.
"x" indicates any amino acid.

W O 97/16S56 PCT~US96/17310 -46- _ TABLE III

Peptides Amino Acid Sequence td4 (K,R)GICEQGSSR
td9 (K,R)TVYHYGK
td9' (K,R)TSTIAYK
td21 (K,R)FGIYR
td33 (K,R)ADIVNQQEILIGRDD*GYYFK
td39 (K,R)ITYVAGKPNGNKVEQGGYPTLAF*
td43 (K,R)MPFAQFPKDCWITFDVAID*TK
td40 (K,R)NLSGYSETAR
td45 KNIAHDKVEKK
td72 KTLSIEEFLALYDR
tdS0 RSYTFSVYIPSSFPDNATTIFAQWHGAPS
RTLVATPEGEIK

The table shows the peptides from tryptic digest of heparinase I. The sequence begins (K,R) because trypsin cuts at either lysine or arginine residues. * represents amino acids that could not be deterrnine~l W O 97/16556 PCT~US96/17310 TABLE IV
MUTANT Kcat (s-l) Products (%~,vild type) C135A 0 none C 13 SD 3.5 ~50 C135E 3.8 ~50 C135S 2 <10 C135H 3 ~so H203A 0 none H203D 3.5 ~10 H203 S 3.2 ~10 H203C 3.9 ~10 KK198AA 4.1 ~50 KK198DD 4.1 ~50 KK198RR 54 equivalent KK208AA 24 ~70 KK208DD 54 equivalent KK208RR 60 equivalent N200A 48 equivalent N200K ~0 none K205A 22 equivalent K205Y ~0 none E207A 18 ~70 D210A 50 equivalent D212A 50 equivalent G213A 20 ~25 K214A 60 equivalent W O 97/16556 PCT~US96/17310 Recomb hep 92 equivalent Native hep 100 CA 0223~223 1998-04-29 W O 97/16556 PCT~US96/17310 ~FFF.R~ENCF~

Andrews, P.C., & Dixon, J.E. (1987) Anal. Biochem. 161:524-528.
Bernstein, H., Yang, V.C., Cooney, C.L., & Langer, R. (1988) Methods in Enz~mol. 137:515-529.
Cardin, A.D., & Weintraub, H.J.R. (1989) Arteriosclerosis 9:21-32 Comfort, A.R., Albert, E., & Langer, R. (1989) Biotech. and Bioeng. 34:1383-1390.
Hammond, B.R., & Gutfreund, H. (1959) Biochem. J. 72:349-353 Har~in~h~m, T.E., & Fosang, A.J. (1992) FASEB J. 6:861-870 Higuchi, R. (1990) PCR Protocols: A Guide to Methods and Applications (Innis, M.A., Gelfand, D.H., Sninsky, J.J., & White, T.J., eds) pp. 177-183, ~c~-lemic Press Inc., NY
Jackson, R.L., Busch, S.J., & Cardin, A.D. (1991) Physiol. Rev. 71:481-539.
Kjellen, L., & T inc1~hl, U. (1991) Annu. Rev. Biochem. 60:443-475.
Kretsinger, R.H. (1975) in Calcium Transport in Contraction and Secretion, Carafoli et al. (eds.), North-Holland Publishing Co., Am~L~,ldall-, pp 469-478.
Kretsinger, R.H. (1980) CRC Crit. Rev. Biochem. 8:119-174.
Laemmli, U.K. (1970) Nature 227:680-685.
Leckband, D., & Langer, R. (1991) Biotech. Bioeng. 37:227-237.
Lee, M.K., & Lander, A.D. (1991) Proc. Natl. Acad. Sci. (USA) 88:2768-2772 Linhardt, R.J., Fitzgerald, G.L., Cooney, C.L., & Langer, R. (1982) Biochem. Biophys. Acta 702: 1 97-203.

Linhardt, R.J., Galliher, P.M., & Cooney, C.L. (1986) Appl. Biochem. Biotechnol. 12:135-176.
Linhardt, R.J., Turnbull, J.E., Wang, H.M., Long~n~thz~n, D., & G~ gher, J.T. (1990) Biochemi~try 29:2611-2617.

Linker, A., & Hoving, P. (1972) Methods in Enzymol. 28:902-911.

Lohse, D.L., & Linhardt, R.J. (1992) J. Biol. Chem. 267:24347-24355.

MacQuarrie, R.A., & Berhard, S.A. (1971) Biochemistry 10:2456-2460 Rabin, B.R., & Watts, D.C. (1960) Nature 188:1163-1165 Sasisekh~r~n, R. (1991) Ph.D. Thesis, Harvard University, Cambridge, MA.

W O 97/16556 PCTrUS96/17310 Sasisekharan, R., Bulmer, M., Moremen, K., Cooney, C.L., & Langer, R. (1993) PrQc. Natl. Acad.
Sci. (USA) 90:3660-3664.
Sasisekharan, R., Moses, M.A., Nugent, M.A., Cooney, C.L., & Langer, R. (1994) Proc. Natl. Acad.
Sci. (USA) 91:1524-1528.
Torchinsky, Yu. M.(1981) Sulfur in Proteins Pergamon Press Inc., N.Y.
Vallee, B., & Riordan, J.F. (1969) Ann. Rev. Biochem. 38:733-794.
Yang, V. C., Linhardt, R.J., Bernstein, H., Cooney, C.L., & Langer, R. (1985) J. Biol. Chem.
260: 1849-1857.

SEQUENOE LIST~NG

(1) GENERAL INFORMATIQN:

(i) APPLICANT: GODAVARTI, R~N~ANATHAN
SASISEKHARAN, R~MNATH
ERNST, STEFFAN
GANESH VENKATARAMAN
COQNEY, CH~RLES L
L~NGER, ROBERT

(ii) TITLE OF INVENTION: RATIONALLY DESIGNED POLYSACCHARIDE
LYASES DERIVED FROM HEPARINASE I

(iii) NUMBER OF SEQUEN OE S: 2 (iv) CORRESPONDENOE ADDRESS:
(A) ADDRESSEE: WOLF, ~K~N~ D & SACKS, P.C.
(B) ~lK~l: 600 ATL~NTIC AVENUE
(C) CITY: BOSTQN
(D) STATE: M~
(E) COUNTRY: USA

(F) ZIP: 02210 (v) COM~Ul~K RE~DABLE FORM:
(A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS

CA 02235223 l998-04-29 WO97/16556 PCTnUS96/17310 (D) SOFTW~RE: P~t~nt Tn Release #1.0, Version #1.25 (vi) CU~NT APPLICATION DATA:
(A) APPLICATION NUMBER:
(B) FILING DATE:
(C) CL~SSIFIC~TION:

(viii) ATTORNEY/AGENT INFORMATION:
(A) NAME: TWOMEY, MICH~EL J.
(B) REGISTR~TION NUMBER: 38,349 (C) K~K~/DOCKET NUMBER: MO656/7014 (ix) TELECOMMUNIC~TION INFORMATION:
(A) TEL~N~: 617-720-3500 (B) TELEFAX: 617-720-2441 (2) INFORMATION FOR SEQ ID NO:1:

(i) ~U~N~ CH~RA~ERISTICS:
(A) LEN~TH: 1379 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYP~l~llCAL: NO

CA 02235223 l998-04-29 (iv) ANTI-SENSE: NO

(vi) ORIGINAL SOUROE :
(A) ORGANISM: DERIVED FROM FLAV~LIERrUM HEPARINUM

(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 173..1327 (ix) FEATURE:
(A) NAME/KEY: misc_~eature (B) LOCATION: 236..1324 (D) OTHER INFORMATION: /product= "MATURE ~ll~"

(xi) SEQUEN OE DESCRIPTION: SEQ ID NO:l:

C~1-111~A GC~GGCA~ AACCATCTCC GAAC~AAGQC AGAACCAGCC TGT~AACAGA 60 CAGCAATTCA TCCGCTTTCA ACCA~AGTGA A~CATTTAA TAC~ATACCA GA~l~l~A 120 'lll~lllC AGCGTACTTT ~ll~lAAAT AACC~ATA~A A~CTA~AGAC GG ATG 175 Met A~A A~A CA~ ATT CTA TAT CTG ATT GTA CTT CAG C~A CTG TTC CTC TGT 223 Lys Lys Gln Ile Leu Tyr Leu Ile Val Leu Gln Gln Leu Phe Leu Cys ~ 5 10 15 CA 02235223 l998-04-29 WO97/165~6 PCT~US96/17310 TCG GCT TAC GCC CAG CAA A~A A~A TCC GGT AAC ATC CCT TAC CGG GTA 271 Ser Ala Tyr Ala Gln Gln Lys Lys Ser Gly Asn Ile Pro Tyr Arg Val AAT GTG CAG GCC GAC AGT GCT A~G CAG A~G GCG ATT ATT GAC AAC A~A 319 Asn Val Gln Ala Asp Ser Ala Lys Gln Lys Ala Ile Ile Asp Asn Lys TGG GTG GCA GTA GGC ATC AAT A~A CCT TAT GCA TTA CAA TAT GAC GAT 367 Trp Val Ala Val Gly Ile Aein Lys Pro Tyr Ala Leu Gln Tyr Asp Asp A~A CTG CGC TTT AAT GGA A~A CCA TCC TAT CGC ll-l GAG CTT A~A GCC 415 Lys Leu Arg Phe Asn Gly Lys Pro Ser Tyr Arg Phe Glu Leu Lys Ala GAA GAC AAT TCG CTT GAA GGT TAT GCT GCA GGA GAA ACA A~G G5C CGT 463 Glu Asp Asn Ser Leu Glu Gly Tyr Ala Ala Gly Glu Thr Lys Gly Arg ACA GAA TTG TCG TAC AGC T~T GCA ACC ACC AAT GAT ~ A~G AAA TTT 511 Thr Glu Leu Ser Tyr Ser Tyr Ala Thr Thr Asn Asp Phe Lys Lys Phe lO0 105 110 CCC CCA AGC GTA TAC CAA A~T GCG CA~ AAG CTA A~A ACC GTT TAT CAT 559 Pro Pro Ser Val Tyr Gln Asn Ala Gln Lys Leu Lys Thr Val Tyr His CA 02235223 l998-04-29 WO97/16556 PCT~US96/17310 TAC GGC AAA GGG ATT TGT GAA CAG GGG AGC TCC CGC AGC TAT ACC 'l~ 607 Tyr Gly Lys Gly Ile Cys Glu Gln Gly Ser Ser Arg Ser Tyr Thr Phe Ser Val Tyr Ile Pro Ser Ser Phe Pro Asp Asn Ala Thr Thr Ile Phe GCC CAA TGG CAT GGT GCA CCC AGC AGA ACG ~'l-l' GTA GCT ACA CCA GAG 703 Ala Gln Trp His Gly Ala Pro Ser Arg Thr Leu Val Ala Thr Pro Glu GGA G~A ATT A~A ACA CTG AGC ATA GAA GAG ~ TTG GCC TTA TAC GAC 751 Gly Glu Ile Lys Thr Leu Ser Ile Glu Glu Phe Leu Ala Leu Tyr Asp CGC ATG ATC TTC A~A A~A A~T ATC GCC CAT GAT A~A GTT GAA A~A A~A 799 Arg Met Ile Phe Lys Lys Asn Ile Ala His Asp Lys Val Glu Lys Lys GAT A~G GAC GGA A~A ATT ACT TAT GTA GCC GGA A~G CCA AAT GGC TGG 847 Asp Lys Asp Gly Lys Ile Thr Tyr Val Ala Gly Lys Pro Asn Gly Trp A~G GTA GAA CAA GGT GGT TAT CCC ACG CTG GCC TTT GGT TTT TCT A~A 895 Lys Val Glu Gln Gly Gly Tyr Pro Thr Leu Ala Phe Gly Phe Ser Lys WO97/165S6 PCTnJS96/17310 GGG TAT l-l-l' TAC ATC A~ GC~ AAC TCC GAC CGG CAG TGG CTT ACC GAC 943 Gly Tyr Phe Tyr Ile Lys Ala Asn Ser Asp Arg Gln Trp Leu Thr Asp A~A GCC GAC CGT A~C AAT GCC AAT CCC GAG AAT AGT GAA GTA ATG A~G 991 Lys Ala Asp Arg Asn Asn Ala Asn Pro Glu Asn Ser Glu Val Met Lys CCC TAT TCC TCG G~A TAC A~A ACT TCA ACC ATT GCC TAT A~A ATG CCC 1039 Pro Tyr Ser Ser Glu Tyr Lys Thr Ser Thr Ile Ala Tyr Lys Met Pro TTT GCC CAG TTC CCT A~A GAT TGC TGG ATT ACT l-ll GAT GTC GCC ATA 1087 Phe Ala Gln Phe Pro Lys Asp Cys Trp Ile Thr Phe Asp Val Ala Ile GAC TGG ACG A~A TAT G~A A~A GAG GCC AAT ACA ATT TTG A~A CCC GGT 1135 Asp Trp Thr Lys Tyr Gly Lys Glu Ala Asn Thr Ile Leu Lys Pro Gly AAG CTG GAT GTG ATG ATG ACT TAT ACC A~G AAT AAG A~A CCA C~A A~A 1183 Lys Leu Asp Val Met Met Thr Tyr Thr Lys Asn Lys Lys Pro Gln Lys GCG CAT ATC GTA A~C CAG CAG GAA ATC CTG ATC GSA CGT AAC GAT GAC 1231 Ala His Ile Val Asn Gln Gln Glu Ile Leu Ile Gly Arg Asn Asp Asp CA 02235223 l998-04-29 WO97/165S6 PCTrUS96/17310 -57-GAT GGC TAT TAC TTC A~A 'l'l-l' GGA ATT TAC AGG GTC GGT A~C AGC ACG 1279 Asp Gly Tyr Tyr Phe Lys Phe Gly Ile Tyr Arg Val Gly Asn Ser Thr GTC CCG GTT ACT TAT A~C CTG AGC GGG TAC AGC G~A ACT GCC AGA TALCP2P~C

Val Pro Val Thr Tyr Asn Leu Ser Gly Tyr Ser Glu Thr Ala Arg CCrA~32GC~ TCCGATAGGG ~ll-l-l~llAT AlllAC~ATA A~ATT 1379 (2) INFORMATION FOR SEQ ID NO:2:

(i) SE~u~ CHAR~TERISTICS:
(A) LENGTH: 384 amino acids (B) TYPE: amino acid (D) TOPOLOGY: 1 in~

( ii ) ~nT .F.~ ~F. TYPE: protein (xi) SEQUEN OE DESCRIPTION: SEQ ID NO:2:

Met Lys Lys Gln Ile Leu Tyr Leu Ile Val Leu Gln Gln Leu Phe Leu Cys Ser Ala Tyr Ala Gln Gln Lys Lys Ser Gly Asn Ile Pro Tyr Arg CA 02235223 l998-04-29 Val Asn Val Gln Ala Asp Ser Ala Lys Gln Lys Ala Ile Ile Asp Asn Lys Trp Val Ala Val Gly Ile Asn Lys Pro Tyr Ala Leu Gln Tyr Asp ~sp Lys Leu Arg Phe Asn Gly Lys Pro Ser Tyr Arg Phe Glu Leu Lys Ala Glu Asp Asn Ser Leu Glu Gly Tyr Ala Ala Gly Glu Thr Lys Gly ~rg Thr Glu Leu Ser Tyr Ser Tyr Ala Thr Thr Asn Asp Phe Lys Lys Phe Pro Pro Ser Val Tyr Gln Asn Ala Gln Lys Leu Lys Thr Val Tyr ~is Tyr Gly Lys Gly Ile Cys Glu Gln Gly Ser Ser Arg Ser Tyr Thr Phe Ser Val Tyr Ile Pro Ser Ser Phe Pro Asp Asn Ala Thr Thr Ile Phe Ala Gln TYP His Gly Ala Pro Ser Arg Thr Leu Val Ala Thr Pro ~lu Gly Glu Ile Lys Thr Leu Ser Ile Glu Glu Phe Leu Ala Leu Tyr CA 0223~223 l998-04-29 WO97/16556 PCT~US96/17310 _59 Asp Arg Met Ile Phe Lys Lys Asn Ile Ala His Asp Lys Val Glu Lys Lys Asp Lys Asp Gly Lys Ile Thr Tyr Val Ala Gly Lys Pro Asn Gly Trp Lys Val Glu Gln Gly Gly Tyr Pro Thr Leu Ala Phe Gly Phe Ser ~ys Gly Tyr Phe Tyr Ile Lys Ala Asn Ser Asp Arg Gln Trp Leu Thr ~sp Lys Ala Asp Arg Asn Asn Ala Asn Pro Glu Asn Ser Glu Val Met Lys Pro Tyr Ser Ser Glu Tyr Lys Thr Ser Thr Ile Ala Tyr Lys Met Pro Phe Ala Gln Phe Pro Lys Asp Cys Trp Ile Thr Phe Asp Val Ala Ile Asp Trp Thr Lys Tyr Gly Lys Glu Ala Asn Thr Ile Leu Lys Pro ~ly Lys Leu Asp Val Met Met Thr Tyr Thr Lys Asn Lys Lys Pro Gln ~ys Ala His Ile Val Asn Gln Gln Glu Ile Leu Ile Gly Arg Asn Asp ~sp Asp Gly Tyr Tyr Phe Lys Phe Gly Ile Tyr Arg Val Gly Asn Ser ~hr Val Pro Val Thr Tyr Asn Leu Ser Gly Tyr Ser Glu Thr Ala Arg

Claims (23)

Claims We claim:

1. A substantially pure polysaccharide lyase comprising the amino acid sequence of the mature peptide of SEQ ID NO: 2 wherein at least one amino acid residue has been substituted and wherein the substitution is selected from the group consisting of (a) a substitution of a cysteine residue corresponding to position 135 of SEQ ID NO: 2 with a residue selected from the group consisting of aspartate, glutamate, serine, threonine, and histidine; (b) a conservative substitution of a residue of a Cardin-Weintraub-like heparin-binding sequence XBBXXXBXB
corresponding to positions 197-205 or 208-212 of SEQ ID NO: 2 with a residue which conforms to the heparin-binding sequence; (c) a conservative substitution of a residue of an EF-hand-like calcium binding sequence corresponding to positions 206-220 of SEQ ID NO: 2 with a residue which conforms to the calcium binding sequence; (d) a conservative substitution of a residue of a PB1, PB2 or PB3 .beta.-sheet domain of SEQ ID NO: 2; (e) a non-conservative substitution of a cysteine residue corresponding to position 297 of SEQ ID NO: 2; (f) a non-conservative substitution of a residue of a PB1, PB2 or PB3 .beta.-sheet domain of SEQ ID NO: 2 which preserves a parallel .beta.-helix tertiary structure characteristic of SEQ ID NO: 2;(g) a deletion of one or more residues of n N-terminal region or a C-terminal region of SEQ ID NO: 2 which preserves a parallel .beta.-helix tertiary structure characteristic of SEQ ID NO: 2; (h) a substitution of a histidine residue corresponding to position 203 of SEQ ID NO: 2 with a residue selected from the group consisting of aspartate, glutamate, serine, threonine and cysteine; (i) a substitution of a lysine residue corresponding to position 198, 199, 205, 208, 209, 211 or 214 of SEQ ID NO: 2 with a residue selected from the group consisting of the small non-polar amino acids, the small polar amino acids, and the acidic amino acids; (j) a substitution of a small polar or small non-polar amino acid for a residue corresponding to a position of SEQ ID NO: 2 selected from the group consisting of Phel 97, Asn200, Asp204, Glu207, Asp210, Asp212 and Gly213; and (k) a non-conservative substitution of a serine residue corresponding to position 39 of SEQ ID NO:2.

2. A substantially pure polysaccharide lyase as in claim 1 wherein the substitution comprises a substitution of a cysteine residue corresponding to position 135 of SEQ ID NO: 2 with a residue selected from the group consisting of aspartate, glutamate, serine, threonine, and histidine.

3 A substantially pure polysaccharide lyase as in claim 2 wherein at least a second amino acid residue has been substituted and wherein the second substitution comprises a conservative substitution of a residue of a Cardin-Weintraub-like heparin binding sequence XBBXXXBXB corresponding to positions 197-205 of SEQ ID NO: 2 with a residue which conforms to the heparin binding sequence.

4 A substantially pure polysaccharide lyase as in claim 2 wherein at least a second amino acid residue has been substituted and wherein the second substitution comprises a conservative substitution of a residue of anEF-hand-like calcium binding sequence corresponding to positions 206-220 with a residue which conforms to the calcium binding sequence.

A substantially pure polysaccharide lyase as in claim 2 wherein at least a second amino acid residue has been substituted and wherein the second substitution comprises a conservative substitution of a residue of a PB1, PB2 or PB3 .beta.-sheet domain of SEQ ID NO: 2.

6. A substantially pure polysaccharide lyase as in claim 1 wherein the substitution comprises a conservative substitution of a residue of a Cardin-Weintraub-like heparin binding sequence XBBXXXBXB corresponding to positions 197-205 of SEQ ID NO: 2 with a residue which conforms to the heparin binding sequence.

7. A substantially pure polysaccharide lyase as in claim 6 wherein the substitution comprises a substitution of a lysine residue corresponding to position 198, 199 or 205 of SEQ ID
NO: 2 with an arginine or histidine.

8. A substantially pure polysaccharide lyase as in claim 6 wherein the substitution comprises a conservative substitution of a histidine residue corresponding to position 203 of SEQ ID
NO: 2.

9. A substantially pure polysaccharide lyase as in claim 1 wherein the substitution comprises a conservative substitution of a residue of an EF-hand-like calcium binding sequence corresponding to positions 206-220 of SEQ ID NO: 2 with a residue which conforms to the calcium binding sequence.

10. A substantially pure polysaccharide lyase as in claim 9 wherein the substitution comprises a substitution of a lysine residue corresponding to position 208, 209, 211 or 214 of SEQ
ID NO: 2 with an arginine or histidine.

11. A substantially pure polysaccharide lyase as in claim 9 wherein the substitution comprises a substitution of an aspartate residue corresponding to positions 210 or 212 of SEQ ID
NO: 2 with a glutamate.

12. A substantially pure polysaccharide lyase as in claim 1 wherein the substitution comprises a substitution of a serine residue corresponding to position 39 of SEQ ID NO: 2 with a alanine residue.

13. A heparin fragment comprising:
a low moleuclar weight heparin fragment greater in size than a hexasaccharide obtainable by the process of incubating with heparin the substantially pure polysaccharide lyase of claim 1 to produce the high order low moleuclar weight heparin fragment.

14. A pharmaceutical preparation comprising a sterile formulation of the substantially pure polysaccharide lyase of claim 1 and a pharmaceutically acceptable carrier.

15. An isolated nucleic acid comprising (a) an isolated nucleic acid encoding the substantially pure polysaccharide lyase of claim 1;
(b) nucleic acids which hybridize under stringent hybridization conditions to the nucleic acid of SEQ ID NO 1 or to the complement of the nucleic acid of SEQ ID NO 1 and which are modified to encode a modified heparinase as described in claim 1; and (c) nucleic acids that differ from the nucleic acids of (b) in codon sequence due to the degeneracy of the genetic code.

16. A recombinant host cell including an isolated nucleic acid as in claim 15.

17. An expression vector including an isolated nucleic acid as in claim 15.

18. A substantially pure polysaccharide lyase comprising:
a modified heparinase having a modified heparinase kcat value, wherein the modified heparinase kcat value is ~75% of a native heparinase kcat value of a complementary native heparinase.

19. An immobilized substantially pure modified heparinase comprising:
a modified heparinase as in claim 18, and a solid support membrane, wherein the modified heparinase is immobilized on the solid support membrane.

20. A substantially pure polysaccharide lyase comprising:
a modified heparinase I having a modified product profile, wherein the modified product profile of the modified heparinase I is ~50% similar to a native product profile of a native heparinase I.

21. A substantially pure polysaccharide lyase comprising:

a modified heparinase I producing when contacted with heparin less than 20% of the disacharrides and trisaccharide as compared to native heparinase I when contacted with the heparin.

22. A method of removing active heparin from a heparin containing fluid comprising:
contacting a heparin containing fluid with the substantially pure polysaccharide lyase as in claims 1, 18, 20 or 21.

23. The method of claim 22 wherein the substantially pure polysaccharide lyase is immobilized on a solid support.