EzCatDB: S00462

DB codeS00462
RLCP classification1.15.9400.1180
CATH domainDomain 13.90.320.10Catalytic domain
E.C.3.1.11.3
CSA1avq


Enzyme Name
Swiss-protKEGG

P03697
Protein nameExonucleaseexodeoxyribonuclease (lambda-induced)
lambda exonuclease
phage lambda-induced exonuclease
Escherichia coli exonuclease IV
E. coli exonuclease IV
exodeoxyribonuclease IV
exonuclease IV
SynonymsEC 3.1.11.3


Swiss-prot:Accession NumberP03697
Entry nameEXO_LAMBD
ActivityExonucleolytic cleavage in the 5''- to 3''- direction to yield nucleoside 5''-phosphates.
SubunitTrimer of three subunits that form a toroid, with a tapered channel passing through the middle.
Subcellular location
CofactorMagnesium.


CofactorsSubstratesProducts
KEGG-idC00305C00039C00001C01150
CompoundmagnesiumDNAH2O5'-Phosphomononucleotides
Typedivalent metal (Ca2+, Mg2+)nucleic acidsH2Onucleotide
1avqAUnboundUnbound
Unbound
1avqBUnboundUnbound
Unbound
1avqCUnboundUnbound
Unbound

Active-site residues
resource
literature [4]
pdbCatalytic residuesCofactor-binding residues
1avqALYS 131
ASP 119;GLU 129 (Mg2+ binding)
1avqBLYS 131
ASP 119;GLU 129 (Mg2+ binding)
1avqCLYS 131
ASP 119;GLU 129 (Mg2+ binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.8, Fig.11, p.12-172
[3]Fig.5, p.13492-134942
[4]p.7895-7896
[5]Fig.1, p.6

references
[1]
CommentsX-ray crystallography (2.4 Angstroms)
PubMed ID9295273
JournalScience
Year1997
Volume277
Pages1824-7
AuthorsKovall R, Matthews BW
TitleToroidal structure of lambda-exonuclease.
Related PDB1avq
[2]
Commentscatalysis
PubMed ID9210460
JournalEur J Biochem
Year1997
Volume246
Pages1-22
AuthorsPingoud A, Jeltsch A
TitleRecognition and cleavage of DNA by type-II restriction endonucleases.
[3]
CommentsX-ray crystallography (2.15 Angstroms)
PubMed ID9811827
JournalProc Natl Acad Sci U S A
Year1998
Volume95
Pages13489-94
AuthorsHorton NC, Newberry KJ, Perona JJ
TitleMetal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.
[4]
CommentsStructural, functional, and evolutionary relationships of the other enzyme
PubMed ID9653111
JournalProc Natl Acad Sci U S A
Year1998
Volume95
Pages7893-7
AuthorsKovall RA, Matthews BW
TitleStructural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.
[5]
PubMed ID10739241
JournalProtein Sci
Year2000
Volume9
Pages1-9
AuthorsDall'Acqua W, Carter P
TitleSubstrate-assisted catalysis: molecular basis and biological significance.

comments
According to the literature [4], the active site of this enzyme is very similar to those of type II endonucleases, such as EcoRV and PvuII. Thus, the paper suggested that the catalytic mechanism can be similar to those of enzymes [4] (see [2] & [3]).
More recent paper [5] supported the substrate-assisted mechanism for the related enzymes (type II restriction enzymes), ruling out the two-metal-ion mechanism. Thus, we concluded that this enzyme adopts the substrate-assisted mechanism with only one metal ion for catalysis (see EcoRV; S00404 in EzCatDB).

createdupdated
2002-07-012009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
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 2010)
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)

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