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
 29108
 		15931
 15931
PubChem 271
 271
 		10298166
 10298166
1dbgA00 Unbound Unbound Unbound Unbound
1dboA00 Unbound Unbound Bound:NGA-GC4-SO4 Unbound
1oflA00 Bound:_CA Unbound Bound:ASG_517-DGC_519 Bound:ASG_520-DGC_522
1ofmA00 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 LYS 250;ARG 271;HIS 272;GLU 333 ASN 213;GLU 243;GLU 245(Calcium binding)
1dboA00 LYS 250;ARG 271;HIS 272;GLU 333 ASN 213;GLU 243;GLU 245(Calcium binding)
1oflA00 LYS 250;ARG 271;HIS 272;GLU 333 ASN 213;GLU 243;GLU 245(Calcium binding)
1ofmA00 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