EzCatDB: S00462
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DB codeS00462
RLCP classification1.15.9400.1180 : Hydrolysis
CATH domainDomain 13.90.320.10 : Lambda Exonuclease; Chain ACatalytic domain
E.C.3.1.11.3
CSA1avq


Enzyme Name
UniProtKBKEGG

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
RefSeqNP_040616.1 (Protein)
NC_001416.1 (DNA/RNA sequence)
PfamPF09588 (YqaJ)
[Graphical view]


UniProtKB: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.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00039C00001C01150
CompoundmagnesiumDNAH2O5'-Phosphomononucleotides
Typedivalent metal (Ca2+, Mg2+)nucleic acidsH2Onucleotide
ChEBI18420

15377

PubChem888

962
22247451

            
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


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