EzCatDB: S00837
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DB codeS00837
RLCP classification5.20.1641500.532 : Elimination
CATH domainDomain 12.160.20.10 : Pectate Lyase C-likeCatalytic domain
E.C.4.2.2.19

CATH domainRelated DB codes (homologues)
2.160.20.10 : Pectate Lyase C-likeS00168,S00171,S00546,S00170,S00169,D00803

Enzyme Name
UniProtKBKEGG

Q46079
Protein nameChondroitinase-BChondroitin B lyase
Chondroitinase B
ChonB
ChnB
SynonymsEC 4.2.2.19
Chondroitin-B lyase
Chondroitin sulfate B lyase
Chondroitin-B eliminase
RefSeqYP_003091073.1 (Protein)
NC_013061.1 (DNA/RNA sequence)
CAZyPL6 (Polysaccharide Lyase Family)


UniProtKB:Accession NumberQ46079
Entry nameCSLB_PEDHE
ActivityEliminative cleavage of dermatan sulfate containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucurosonyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups to yield a 4,5-unsaturated dermatan-sulfate disaccharide (DUA-GalNAc-4S).
SubunitMonomer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00076L00055L00055C04864
CompoundCalciumDermatan sulfateDermatan sulfate4-Deoxy-beta-D-gluc-4-enuronosyl-(1,3)-N-acetyl-D-galactosamine 4-sulfate
Typedivalent metal (Ca2+, Mg2+)amide group,carboxyl group,polysaccharide,sulfate groupamide group,carboxyl group,polysaccharide,sulfate groupamide group,carboxyl group,polysaccharide,sulfate group
ChEBI29108


15931
PubChem271


10298166
            
1dbgA00UnboundUnboundUnboundUnbound
1dboA00UnboundUnboundBound:NGA-GC4-SO4Unbound
1oflA00Bound:_CAUnboundBound:ASG 517-DGC 519Bound:ASG 520-DGC 522
1ofmA00UnboundUnboundBound:ASG-BDP-ASG-DGCUnbound

Active-site residues
resource
Literature [4], [6], [7] & Swiss-prot;Q46079
pdbCatalytic residuesCofactor-binding residues
          
1dbgA00LYS 250;ARG 271;HIS 272;GLU 333
ASN 213;GLU 243;GLU 245(Calcium binding)
1dboA00LYS 250;ARG 271;HIS 272;GLU 333
ASN 213;GLU 243;GLU 245(Calcium binding)
1oflA00LYS 250;ARG 271;HIS 272;GLU 333
ASN 213;GLU 243;GLU 245(Calcium binding)
1ofmA00LYS 250;ARG 271;HIS 272;GLU 333
ASN 213;GLU 243;GLU 245(Calcium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Figure 5
[6]

[7]FIG. 7, p.32893-32895

references
[1]
PubMed ID2158
JournalBiochem J
Year1975
Volume151
Pages121-9
AuthorsMichelacci YM, Dietrich CP
TitleA comparative study between a chondroitinase B and a chondroitinase AC from Flavobacterium heparinum: Isolation of a chondroitinase AC-susceptible dodecasaccharide from chondroitin sulphate B.
[2]
JournalFEBS Lett
Year1987
Volume212
Pages199-202
AuthorsGacesa P
TitleAlginate-modifying enzymes: A proposed unified mechanism of action for the lyases and epimerases.
[3]
PubMed ID8526872
JournalBiochem J
Year1995
Volume312
Pages569-77
AuthorsGu K, Linhardt RJ, Laliberte M, Gu K, Zimmermann J
TitlePurification, characterization and specificity of chondroitin lyases and glycuronidase from Flavobacterium heparinum.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
PubMed ID10600383
JournalJ Mol Biol
Year1999
Volume294
Pages1257-69
AuthorsHuang W, Matte A, Li Y, Kim YS, Linhardt RJ, Su H, Cygler M
TitleCrystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution.
Related PDB1dbg,1dbo
Related UniProtKBQ46079
[5]
PubMed ID11500043
JournalBiochem Biophys Res Commun
Year2001
Volume286
Pages343-51
AuthorsPojasek K, Shriver Z, Kiley P, Venkataraman G, Sasisekharan R
TitleRecombinant expression, purification, and kinetic characterization of chondroitinase AC and chondroitinase B from Flavobacterium heparinum.
[6]
CommentsCHARACTERIZATION, MUTAGENESIS OF LYS-250; HIS-272; GLU-333; ARG-363 AND ARG-364.
PubMed ID12063249
JournalJ Biol Chem
Year2002
Volume277
Pages31179-86
AuthorsPojasek K, Raman R, Kiley P, Venkataraman G, Sasisekharan R
TitleBiochemical characterization of the chondroitinase B active site.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
PubMed ID15155751
JournalJ Biol Chem
Year2004
Volume279
Pages32882-96
AuthorsMichel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M
TitleThe structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
Related PDB1ofl,1ofm
Related UniProtKBQ46079

comments
This enzyme belongs to polysaccharide lyase family-6.
Although literature [7] suggested that Arg271 might act as a general acid to protonate the O1 atom of GalNAc-4S in the departing dermatan sulfate, it is unlikely to be a general acid. Instead, Glu333 may act as a general acid to protonate the O1 atom, throuhg a nearby water, considering the active site structure. Thus, the reaction of this enzyme seems to proceed as follows (see [4], [6] and [7]):
(0) This elimination reaction may proceed through the E1cb pathway, rather than the E1 pathway.
(1) Calcium ion, which is bound to Asn213, Glu243 and Glu245, stabilizes the carboxylate of L-iduronic acid (idoA) at the +1 subsite, lowering the pKa of the C5 atom of idoA.
(2) Lys250 acts as a general base to deprotonate the C5 atom, giving a carbanion intermediate.
(3) Whilst Arg271 stabilizes the developing negative charge on the O1 atom of GalNAc-4S at the -1 subsite (in the departing dermatan sulfate), Glu333 may act as a general acid to protonate the O1 atom through a water molecule.

createdupdated
2010-05-262011-11-11


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