DB code: D00511

CATH domain 1.10.1670.10 : Endonuclease Iii, domain 2
1.10.340.30 : Endonuclease III; domain 1
E.C. 3.2.2.- 4.2.99.18
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.1670.10 : Endonuclease Iii, domain 2 T00070 D00266
1.10.340.30 : Endonuclease III; domain 1 S00749 T00070 D00266

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q8U2D5 N-glycosylase/DNA lyase
8-oxoguanine DNA glycosylase
EC 3.2.2.-
AGOG
DNA-(apurinic or apyrimidinic site) lyase
AP lyase
EC 4.2.99.18
NP_578633.2 (Protein)
NC_003413.1 (DNA/RNA sequence)
PF09171 (DUF1886)
[Graphical View]
Q8ZVK6 N-glycosylase/DNA lyase
8-oxoguanine DNA glycosylase
EC 3.2.2.-
AGOG
DNA-(apurinic or apyrimidinic site) lyase
AP lyase
EC 4.2.99.18
Pa-AGOG
NP_559868.1 (Protein)
NC_003364.1 (DNA/RNA sequence)
PF09171 (DUF1886)
[Graphical View]

KEGG enzyme name
DNA-(apurinic or apyrimidinic site) lyase
(EC 4.2.99.18 )
AP lyase
(EC 4.2.99.18 )
AP endonuclease class I
(EC 4.2.99.18 )
endodeoxyribonuclease (apurinic or apyrimidinic)
(EC 4.2.99.18 )
deoxyribonuclease (apurinic or apyrimidinic)
(EC 4.2.99.18 )
E. coli endonuclease III
(EC 4.2.99.18 )
phage-T4 UV endonuclease
(EC 4.2.99.18 )
Micrococcus luteus UV endonuclease
(EC 4.2.99.18 )
AP site-DNA 5'-phosphomonoester-lyase
(EC 4.2.99.18 )
X-ray endonuclease III
(EC 4.2.99.18 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q8U2D5 AGOG_PYRFU The C-O-P bond 3'' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3''-terminal unsaturated sugar and a product with a terminal 5''-phosphate.
Q8ZVK6 AGOG_PYRAE The C-O-P bond 3'' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3''-terminal unsaturated sugar and a product with a terminal 5''-phosphate.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C02270 C03484 C00578 L00013
E.C. 4.2.99.18
4.2.99.18
4.2.99.18
4.2.99.18
Compound Base-removed DNA Apyrimidinic site in DNA DNA 5'-phosphate DNA 3'-trans-alpha,beta unsaturated aldehyde
Type carbohydrate,nucleic acids,phosphate group/phosphate ion nucleic acids nucleic acids,phosphate group/phosphate ion nucleic acids,carbohydrate
ChEBI
PubChem
1xg7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1xg7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1xqoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1xqpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:8HG_255 Unbound Unbound Unbound
1xg7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1xg7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1xqoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1xqpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2], [3]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1xg7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 176
1xg7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 176
1xqoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 172
1xqpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 172
1xg7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 144
1xg7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 144
1xqoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 140
1xqpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 140

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.1, p.1646-1647
[3]
p.96

References
[1]
Resource
Comments
Medline ID
PubMed ID 15604455
Journal Nucleic Acids Res
Year 2004
Volume 32
Pages 6531-9
Authors Sartori AA, Lingaraju GM, Hunziker P, Winkler FK, Jiricny J
Title Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases.
Related PDB
Related UniProtKB Q8ZVK6
[2]
Resource
Comments
Medline ID
PubMed ID 15610848
Journal Chem Biol
Year 2004
Volume 11
Pages 1643-9
Authors Chung SJ, Verdine GL
Title Structures of end products resulting from lesion processing by a DNA glycosylase/lyase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 15642264
Journal Structure
Year 2005
Volume 13
Pages 87-98
Authors Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK
Title A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.
Related PDB 1xqo 1xqp
Related UniProtKB Q8ZVK6

Comments
E.C. 3.1.25.2 was transferred to E.C. 4.2.99.18.
This enzyme is homologous to hOgg1 (PDB; 1m3h, 1m3q), and probably catalyzes similar reactions to those by hOgg1. The literature [2] suggests the catalytic mechanism of hOgg1.
According to the literature [2] and [3], this enzyme catalyzes the following reactions:
(A) Transfer of DNA deoxyribose from DNA base nitrogen atom to sidechain of Lysine residue:
(B) Intramolecular elimination (Sugar opening) leading to Schiff-base formation on Lysine residue:
(C) Isomerization (Shift of double-bond):
(D) Elimination of 5'-phosphate of DNA leading to formation of alpha,beta-unsaturated Schiff base and DNA-5'-phosphate:
(E) Deformation of Schiff-base from Lysine residue:
However, the detailed mechanism has not been elucidated yet.

Created Updated
2004-07-21 2009-02-26