EzCatDB: D00518
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DB codeD00518
RLCP classification5.20.8010.94 : Elimination
CATH domainDomain 11.50.10.110 : GlycosyltransferaseCatalytic domain
Domain 22.60.-.-
E.C.4.2.2.3
CSA1qaz


Enzyme Name
UniProtKBKEGG

Q9KWU1
Protein name
poly(beta-D-mannuronate) lyase
alginate lyase I
alginate lyase
alginase I
alginase II
alginase
poly(beta-D-1,4-mannuronide) lyase
SynonymsAlginate lyase
PfamPF05426 (Alginate_lyase)
PF08787 (Alginate_lyase2)
[Graphical view]
CAZyPL5 (Polysaccharide Lyase Family)
PL7 (Polysaccharide Lyase Family)

KEGG pathways
MAP codePathways
MAP00051Fructose and mannose metabolism

UniProtKB:Accession NumberQ9KWU1
Entry nameQ9KWU1_9SPHN
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC01768C01768C04662
Compound(Alginate)n+1(Alginate)n4-Deoxy-alpha-L-erythro-hex-4-enopyranuronoside
Typecarboxyl group,polysaccharidecarboxyl group,polysaccharidecarbohydrate,carboxyl group
ChEBI


PubChem


           
1qazAUnboundUnboundUnbound
1hv6AUnboundBound:MAW-MAV-GCUUnbound

Active-site residues
resource
literature [2]
pdbCatalytic residues
         
1qazAHIS 192;ARG 239;TYR 246
1hv6AHIS 192;ARG 239;TYR 246

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.4b, p.14-15

references
[1]
CommentsX-ray crystallography
PubMed ID10390348
JournalJ Mol Biol
Year1999
Volume290
Pages505-14
AuthorsYoon HJ, Mikami B, Hashimoto W, Murata K
TitleCrystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.
Related PDB1qaz
[2]
CommentsX-ray crystallography
PubMed ID11243798
JournalJ Mol Biol
Year2001
Volume307
Pages9-16
AuthorsYoon HJ, Hashimoto W, Miyake O, Murata K, Mikami B
TitleCrystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0 A resolution.
Related PDB1hv6
[3]
PubMed ID12729723
JournalProtein Expr Purif
Year2003
Volume29
Pages33-41
AuthorsMiyake O, Hashimoto W, Murata K
TitleAn exotype alginate lyase in Sphingomonas sp. A1: overexpression in Escherichia coli, purification, and characterization of alginate lyase IV (A1-IV).
[4]
PubMed ID15136569
JournalJ Biol Chem
Year2004
Volume279
Pages31863-72
AuthorsYamasaki M, Moriwaki S, Miyake O, Hashimoto W, Murata K, Mikami B
TitleStructure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
[5]
PubMed ID15644208
JournalJ Mol Biol
Year2005
Volume345
Pages1111-8
AuthorsOsawa T, Matsubara Y, Muramatsu T, Kimura M, Kakuta Y
TitleCrystal structure of the alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. at 1.2 A resolution.

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.

createdupdated
2005-02-232009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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