DB code: S00837

RLCP classification 5.20.1641500.532 : Elimination
CATH domain 2.160.20.10 : Pectate Lyase C-like Catalytic domain
E.C. 4.2.2.19
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.160.20.10 : Pectate Lyase C-like S00168 S00171 S00546 S00170 S00169 D00803

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq CAZy
Q46079 Chondroitinase-B
EC 4.2.2.19
Chondroitin-B lyase
Chondroitin sulfate B lyase
Chondroitin-B eliminase
YP_003091073.1 (Protein)
NC_013061.1 (DNA/RNA sequence)
PL6 (Polysaccharide Lyase Family 6)

KEGG enzyme name
Chondroitin B lyase
Chondroitinase B
ChonB
ChnB

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q46079 CSLB_PEDHE Eliminative 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). Monomer.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00076 L00055 L00055 C04864
E.C.
Compound Calcium Dermatan sulfate Dermatan sulfate 4-Deoxy-beta-D-gluc-4-enuronosyl-(1,3)-N-acetyl-D-galactosamine 4-sulfate
Type divalent metal (Ca2+, Mg2+) amide group,carboxyl group,polysaccharide,sulfate group amide group,carboxyl group,polysaccharide,sulfate group amide group,carboxyl group,polysaccharide,sulfate group
ChEBI 29108
15931
PubChem 271
10298166
1dbgA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1dboA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:NGA-GC4-SO4 Unbound
1oflA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Bound:ASG_517-DGC_519 Bound:ASG_520-DGC_522
1ofmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ASG-BDP-ASG-DGC Unbound

Reference for Active-site residues
resource references E.C.
Literature [4], [6], [7] & Swiss-prot;Q46079

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dbgA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 250;ARG 271;HIS 272;GLU 333 ASN 213;GLU 243;GLU 245(Calcium binding)
1dboA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 250;ARG 271;HIS 272;GLU 333 ASN 213;GLU 243;GLU 245(Calcium binding)
1oflA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 250;ARG 271;HIS 272;GLU 333 ASN 213;GLU 243;GLU 245(Calcium binding)
1ofmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 250;ARG 271;HIS 272;GLU 333 ASN 213;GLU 243;GLU 245(Calcium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Figure 5
[6]
[7]
FIG. 7, p.32893-32895

References
[1]
Resource
Comments
Medline ID
PubMed ID 2158
Journal Biochem J
Year 1975
Volume 151
Pages 121-9
Authors Michelacci YM, Dietrich CP
Title A comparative study between a chondroitinase B and a chondroitinase AC from Flavobacterium heparinum: Isolation of a chondroitinase AC-susceptible dodecasaccharide from chondroitin sulphate B.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID
Journal FEBS Lett
Year 1987
Volume 212
Pages 199-202
Authors Gacesa P
Title Alginate-modifying enzymes: A proposed unified mechanism of action for the lyases and epimerases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8526872
Journal Biochem J
Year 1995
Volume 312
Pages 569-77
Authors Gu K, Linhardt RJ, Laliberte M, Gu K, Zimmermann J
Title Purification, characterization and specificity of chondroitin lyases and glycuronidase from Flavobacterium heparinum.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
Medline ID
PubMed ID 10600383
Journal J Mol Biol
Year 1999
Volume 294
Pages 1257-69
Authors Huang W, Matte A, Li Y, Kim YS, Linhardt RJ, Su H, Cygler M
Title Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution.
Related PDB 1dbg 1dbo
Related UniProtKB Q46079
[5]
Resource
Comments
Medline ID
PubMed ID 11500043
Journal Biochem Biophys Res Commun
Year 2001
Volume 286
Pages 343-51
Authors Pojasek K, Shriver Z, Kiley P, Venkataraman G, Sasisekharan R
Title Recombinant expression, purification, and kinetic characterization of chondroitinase AC and chondroitinase B from Flavobacterium heparinum.
Related PDB
Related UniProtKB
[6]
Resource
Comments CHARACTERIZATION, MUTAGENESIS OF LYS-250; HIS-272; GLU-333; ARG-363 AND ARG-364.
Medline ID
PubMed ID 12063249
Journal J Biol Chem
Year 2002
Volume 277
Pages 31179-86
Authors Pojasek K, Raman R, Kiley P, Venkataraman G, Sasisekharan R
Title Biochemical characterization of the chondroitinase B active site.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
Medline ID
PubMed ID 15155751
Journal J Biol Chem
Year 2004
Volume 279
Pages 32882-96
Authors Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M
Title The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
Related PDB 1ofl 1ofm
Related UniProtKB Q46079

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.

Created Updated
2010-05-26 2011-11-11