3KNT | pdb_00003knt

Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	HhH-GPD_1	e3kntD1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD_1	ECOD (1.6)
C	HhH-GPD_1	e3kntC1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD_1	ECOD (1.6)
B	HhH-GPD_1	e3kntB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD_1	ECOD (1.6)
A	HhH-GPD_1	e3kntA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.1670.10	Mainly Alpha	Orthogonal Bundle	Endonuclease Iii, domain 2	Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)	CATH (4.3.0)
D	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)
C	1.10.1670.10	Mainly Alpha	Orthogonal Bundle	Endonuclease Iii, domain 2	Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)	CATH (4.3.0)
C	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)
B	1.10.1670.10	Mainly Alpha	Orthogonal Bundle	Endonuclease Iii, domain 2	Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)	CATH (4.3.0)
B	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)
A	1.10.1670.10	Mainly Alpha	Orthogonal Bundle	Endonuclease Iii, domain 2	Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)	CATH (4.3.0)
A	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF22175	8-oxoguanine DNA glycosylase (Ogg-HhH)	8-oxoguanine DNA glycosylase	This entry represents 8-oxoguanine DNA glycosylases (Ogg) that are responsible for the recognition and excision of one of the most common DNA oxidative product, 7,8-dihydro-8-oxoguanine (8-oxoG). These enzymes share a common all-alpha architecture bu ...	This entry represents 8-oxoguanine DNA glycosylases (Ogg) that are responsible for the recognition and excision of one of the most common DNA oxidative product, 7,8-dihydro-8-oxoguanine (8-oxoG). These enzymes share a common all-alpha architecture build around a central HhH motif [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, H, J, L	5'-D(TPGPGPTPAPGPAPCPCPTPGPGPAPCP*G)-3'	-	-	-
E, G, I, K	5'-D(APCPGPTPCPCPAP(8OG)PGPTPCPTPAPCP*C)-3'	-	-	-
A, B, C, D	N-glycosylase/DNA lyase	DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012092	8-oxoguanine DNA glycosylase/AP lyase Ogg	Family
A, B, C, D	IPR003265	HhH-GPD domain	Domain
A, B, C, D	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal	Homologous Superfamily
A, B, C, D	IPR011257	DNA glycosylase	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.