3VK8 | pdb_00003vk8

Crystal structure of DNA-glycosylase bound to DNA containing Thymine glycol

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)
B	Peptidase_M14	e3vk8B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Peptidase_M14	ECOD (v294.1)
A	Peptidase_M14	e3vk8A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Peptidase_M14	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.190.10	Alpha Beta	Alpha-Beta Barrel	N-terminal domain of MutM-like DNA repair proteins	MutM-like, N-terminal	CATH (4.3.0)
B	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.20.190.10	Alpha Beta	Alpha-Beta Barrel	N-terminal domain of MutM-like DNA repair proteins	MutM-like, N-terminal	CATH (4.3.0)
A	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21025	Formamidopyrimidine-DNA glycosylase C-terminal domain (Fapy_DNA_glyco_C)	Formamidopyrimidine-DNA glycosylase C-terminal domain	This entry represents a small C-terminal zinc finger domain found in a small subset of Formamidopyrimidine-DNA glycosylase enzymes.	Domain
A, B	PF06831	Formamidopyrimidine-DNA glycosylase H2TH domain (H2TH)	Formamidopyrimidine-DNA glycosylase H2TH domain	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F	DNA (5'-D(CPGPTPCPCPAP(CTG)PGPTPCPTPAP*C)-3')	-	-	-
C, E	DNA (5'-D(GPTPAPGPAPCPCPTPGPGPAPCP*G)-3')	-	-	-
A, B	Probable formamidopyrimidine-DNA glycosylase	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 cation binding transition metal ion binding zinc ion binding 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 cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity oxidized purine nucleobase lesion DNA N-glycosylase activity hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds DNA binding damaged DNA binding nucleic acid binding	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	IPR035937	Formamidopyrimidine-DNA glycosylase, N-terminal	Homologous Superfamily
A, B	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain	Domain
A, B	IPR015886	Formamidopyrimidine-DNA glycosylase, H2TH DNA-binding	Domain
A, B	IPR049392	Formamidopyrimidine-DNA glycosylase, C-terminal domain	Domain
A, B	IPR010979	Small ribosomal subunit protein uS13-like, H2TH	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.