DB code: D00518

RLCP classification 5.20.8010.94 : Elimination
CATH domain 1.50.10.110 : Glycosyltransferase Catalytic domain
2.60.-.- :
E.C. 4.2.2.3
CSA 1qaz
M-CSA 1qaz
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
Q9KWU1
Alginate lyase
PL5 (Polysaccharide Lyase Family 5)
PL7 (Polysaccharide Lyase Family 7)
PF05426 (Alginate_lyase)
PF08787 (Alginate_lyase2)
[Graphical View]

KEGG enzyme name
poly(beta-D-mannuronate) lyase
alginate lyase I
alginate lyase
alginase I
alginase II
alginase
poly(beta-D-1,4-mannuronide) lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q9KWU1 Q9KWU1_9SPHN

KEGG Pathways
Map code Pathways E.C.
MAP00051 Fructose and mannose metabolism

Compound table
Substrates Products Intermediates
KEGG-id C01768 C01768 C04662
E.C.
Compound (Alginate)n+1 (Alginate)n 4-Deoxy-alpha-L-erythro-hex-4-enopyranuronoside
Type carboxyl group,polysaccharide carboxyl group,polysaccharide carbohydrate,carboxyl group
ChEBI
PubChem
1qazA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1hv6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:MAW-MAV-GCU Unbound

Reference for Active-site residues
resource references E.C.
literature [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1qazA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 192;ARG 239;TYR 246
1hv6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 192;ARG 239;TYR 246

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.4b, p.14-15

References
[1]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10390348
Journal J Mol Biol
Year 1999
Volume 290
Pages 505-14
Authors Yoon HJ, Mikami B, Hashimoto W, Murata K
Title Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.
Related PDB 1qaz
Related UniProtKB
[2]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11243798
Journal J Mol Biol
Year 2001
Volume 307
Pages 9-16
Authors Yoon HJ, Hashimoto W, Miyake O, Murata K, Mikami B
Title Crystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0 A resolution.
Related PDB 1hv6
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 12729723
Journal Protein Expr Purif
Year 2003
Volume 29
Pages 33-41
Authors Miyake O, Hashimoto W, Murata K
Title An exotype alginate lyase in Sphingomonas sp. A1: overexpression in Escherichia coli, purification, and characterization of alginate lyase IV (A1-IV).
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 15136569
Journal J Biol Chem
Year 2004
Volume 279
Pages 31863-72
Authors Yamasaki M, Moriwaki S, Miyake O, Hashimoto W, Murata K, Mikami B
Title Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 15644208
Journal J Mol Biol
Year 2005
Volume 345
Pages 1111-8
Authors Osawa T, Matsubara Y, Muramatsu T, Kimura M, Kakuta Y
Title Crystal structure of the alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. at 1.2 A resolution.
Related PDB
Related UniProtKB

Comments
This enzyme is composed of two domains. However, only the tertiary structures of the N-terminal domain have been reported.
The literature [2] proposed a catalytic mechanism as follows:
(1) The ionized sidechain of Tyr246 is stabilized by the positive charge of Arg239. This ionized Tyr246 acts as a general base, which abstracts a proton from C-5 atom of the leaving group of the substrate (at subsite +1), resulting in a formation of a carboxylate dianion intermediate.
(2) His192 stabilizes the dianion intermediate.
(3) Tyr246 acts as a general acid to protonate the oxygen of the glycoside bond (eliminated group), resulting in the formation of a double-bond between C-4 and C-5 atoms and the cleavage of the bond.

Created Updated
2005-02-23 2009-02-26