DB code: S00462

RLCP classification 1.15.9400.1180 : Hydrolysis
CATH domain 3.90.320.10 : Lambda Exonuclease; Chain A Catalytic domain
E.C. 3.1.11.3
CSA 1avq
M-CSA 1avq
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P03697 Exonuclease
EC 3.1.11.3
NP_040616.1 (Protein)
NC_001416.1 (DNA/RNA sequence)
PF09588 (YqaJ)
[Graphical View]

KEGG enzyme name
exodeoxyribonuclease (lambda-induced)
lambda exonuclease
phage lambda-induced exonuclease
Escherichia coli exonuclease IV
E. coli exonuclease IV
exodeoxyribonuclease IV
exonuclease IV

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P03697 EXO_LAMBD Exonucleolytic cleavage in the 5''- to 3''- direction to yield nucleoside 5''-phosphates. Trimer of three subunits that form a toroid, with a tapered channel passing through the middle. Magnesium.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00039 C00001 C01150
E.C.
Compound magnesium DNA H2O 5'-Phosphomononucleotides
Type divalent metal (Ca2+, Mg2+) nucleic acids H2O
ChEBI 18420
15377
PubChem 888
22247451
962
1avqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1avqB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1avqC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1avqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 131 ASP 119;GLU 129 (Mg2+ binding)
1avqB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 131 ASP 119;GLU 129 (Mg2+ binding)
1avqC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 131 ASP 119;GLU 129 (Mg2+ binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.8, Fig.11, p.12-17 2
[3]
Fig.5, p.13492-13494 2
[4]
p.7895-7896
[5]
Fig.1, p.6

References
[1]
Resource
Comments X-ray crystallography (2.4 Angstroms)
Medline ID
PubMed ID 9295273
Journal Science
Year 1997
Volume 277
Pages 1824-7
Authors Kovall R, Matthews BW
Title Toroidal structure of lambda-exonuclease.
Related PDB 1avq
Related UniProtKB
[2]
Resource
Comments catalysis
Medline ID
PubMed ID 9210460
Journal Eur J Biochem
Year 1997
Volume 246
Pages 1-22
Authors Pingoud A, Jeltsch A
Title Recognition and cleavage of DNA by type-II restriction endonucleases.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-ray crystallography (2.15 Angstroms)
Medline ID
PubMed ID 9811827
Journal Proc Natl Acad Sci U S A
Year 1998
Volume 95
Pages 13489-94
Authors Horton NC, Newberry KJ, Perona JJ
Title Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.
Related PDB
Related UniProtKB
[4]
Resource
Comments Structural, functional, and evolutionary relationships of the other enzyme
Medline ID
PubMed ID 9653111
Journal Proc Natl Acad Sci U S A
Year 1998
Volume 95
Pages 7893-7
Authors Kovall RA, Matthews BW
Title Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10739241
Journal Protein Sci
Year 2000
Volume 9
Pages 1-9
Authors Dall'Acqua W, Carter P
Title Substrate-assisted catalysis: molecular basis and biological significance.
Related PDB
Related UniProtKB

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).

Created Updated
2002-07-01 2009-02-26