4YPR | pdb_00004ypr

Crystal Structure of D144N MutY bound to its anti-substrate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DNA-glycosylase	8040877	3000905	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8040880	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8040880	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-glycosylase	8040877	3000905	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	RPE65	e4yprB1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: RPE65	ECOD (v294.1)
A	RPE65	e4yprA1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: RPE65	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	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)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F	DNA (5'-D(APAPGPAPCP(8OG)PTPGPGPAP*C)-3')	-	-	-
C, E	DNA (5'-D(TGPTPCPCPAPCPGPTPCP*T)-3')	-	-	-
A, B	A/G-specific adenine glycosylase	hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid oxidized purine nucleobase lesion DNA N-glycosylase activity hydrolase activity 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA binding adenine/guanine mispair binding double-stranded DNA binding binding hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid oxidized purine nucleobase lesion DNA N-glycosylase activity hydrolase activity 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA binding adenine/guanine mispair binding double-stranded DNA binding binding mismatched DNA binding nucleic acid binding purine-specific mismatch base pair DNA N-glycosylase activity mismatch base pair DNA N-glycosylase activity oxidized DNA binding oxidized purine DNA binding damaged DNA binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion 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 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 mismatch repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003265	HhH-GPD domain	Domain
A, B	IPR000445	Helix-hairpin-helix motif	Conserved Site
A, B	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal	Homologous Superfamily
A, B	IPR044298	Adenine/Thymine-DNA glycosylase	Family
A, B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B	IPR029119	Adenine DNA glycosylase, C-terminal	Domain
A, B	IPR005760	A/G-specific adenine glycosylase MutY	Family
A, B	IPR011257	DNA glycosylase	Homologous Superfamily
A, B	IPR003651	Endonuclease III-like, iron-sulphur cluster loop motif	Conserved Site

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.