EzCatDB: D00511
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DB codeD00511
CATH domainDomain 11.10.1670.10 : Endonuclease Iii, domain 2
Domain 21.10.340.30 : Endonuclease III; domain 1
E.C.3.2.2.-,4.2.99.18

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

Enzyme Name
UniProtKBKEGG

Q8U2D5Q8ZVK6
Protein nameN-glycosylase/DNA lyaseN-glycosylase/DNA lyaseDNA-(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)

Synonyms8-oxoguanine DNA glycosylase
EC 3.2.2.-
AGOG
DNA-(apurinic or apyrimidinic site) lyase
AP lyase
EC 4.2.99.18
8-oxoguanine DNA glycosylase
EC 3.2.2.-
AGOG
DNA-(apurinic or apyrimidinic site) lyase
AP lyase
EC 4.2.99.18
Pa-AGOG
RefSeqNP_578633.2 (Protein)
NC_003413.1 (DNA/RNA sequence)
NP_559868.1 (Protein)
NC_003364.1 (DNA/RNA sequence)
PfamPF09171 (DUF1886)
[Graphical view]
PF09171 (DUF1886)
[Graphical view]


UniProtKB:Accession NumberQ8U2D5Q8ZVK6
Entry nameAGOG_PYRFUAGOG_PYRAE
ActivityThe 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.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.
Subunit

Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC02270C03484C00578L00013
E.C.4.2.99.184.2.99.184.2.99.184.2.99.18
CompoundBase-removed DNAApyrimidinic site in DNADNA 5'-phosphateDNA 3'-trans-alpha,beta unsaturated aldehyde
Typecarbohydrate,nucleic acids,phosphate group/phosphate ionnucleic acidsnucleic acids,phosphate group/phosphate ionnucleic acids,carbohydrate
ChEBI



PubChem



            
1xg7A01UnboundUnboundUnboundUnbound
1xg7B01UnboundUnboundUnboundUnbound
1xqoA01UnboundUnboundUnboundUnbound
1xqpA01Analogue:8HG 255UnboundUnboundUnbound
1xg7A02UnboundUnboundUnboundUnbound
1xg7B02UnboundUnboundUnboundUnbound
1xqoA02UnboundUnboundUnboundUnbound
1xqpA02UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [2], [3]
pdbCatalytic residues
         
1xg7A01ASP 176
1xg7B01ASP 176
1xqoA01ASP 172
1xqpA01ASP 172
1xg7A02LYS 144
1xg7B02LYS 144
1xqoA02LYS 140
1xqpA02LYS 140

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.1, p.1646-1647
[3]p.96

references
[1]
PubMed ID15604455
JournalNucleic Acids Res
Year2004
Volume32
Pages6531-9
AuthorsSartori AA, Lingaraju GM, Hunziker P, Winkler FK, Jiricny J
TitlePa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases.
Related UniProtKBQ8ZVK6
[2]
PubMed ID15610848
JournalChem Biol
Year2004
Volume11
Pages1643-9
AuthorsChung SJ, Verdine GL
TitleStructures of end products resulting from lesion processing by a DNA glycosylase/lyase.
[3]
PubMed ID15642264
JournalStructure
Year2005
Volume13
Pages87-98
AuthorsLingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK
TitleA DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.
Related PDB1xqo,1xqp
Related UniProtKBQ8ZVK6

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.

createdupdated
2004-07-212009-02-26


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 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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