2OQ4 | pdb_00002oq4

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth B]	d2oq4b1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Middle domain of MutM-like DNA repair proteins	Endonuclease VIII	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth B]	d2oq4b2	All beta proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	Endonuclease VIII	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth B]	d2oq4b3	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	C-terminal, Zn-finger domain of MutM-like DNA repair proteins	Endonuclease VIII	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth A]	d2oq4a1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Middle domain of MutM-like DNA repair proteins	Endonuclease VIII	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth A]	d2oq4a2	All beta proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	Endonuclease VIII	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth A]	d2oq4a3	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	C-terminal, Zn-finger domain of MutM-like DNA repair proteins	Endonuclease VIII	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth B]	SCOP2B Superfamily	FPG N-terminal domain-like	8056354	3000074	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	S13-like H2TH domain	8056355	3000053	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056356	3000068	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	S13-like H2TH domain	8056355	3000053	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	FPG N-terminal domain-like	8056354	3000074	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056356	3000068	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)
F [auth B]	Fapy_DNA_glyco	e2oq4B1	A: beta barrels	X: MutM N-terminal domain-like	H: N-terminal domain of MutM-like DNA repair proteins (From Topology)	T: N-terminal domain of MutM-like DNA repair proteins	F: Fapy_DNA_glyco	ECOD (1.6)
F [auth B]	H2TH	e2oq4B2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
F [auth B]	zf-FPG_IleRS	e2oq4B3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: C-terminal, Zn-finger domain of MutM-like DNA repair proteins (From Topology)	T: C-terminal, Zn-finger domain of MutM-like DNA repair proteins	F: zf-FPG_IleRS	ECOD (1.6)
E [auth A]	Fapy_DNA_glyco	e2oq4A1	A: beta barrels	X: MutM N-terminal domain-like	H: N-terminal domain of MutM-like DNA repair proteins (From Topology)	T: N-terminal domain of MutM-like DNA repair proteins	F: Fapy_DNA_glyco	ECOD (1.6)
E [auth A]	H2TH	e2oq4A2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
E [auth A]	zf-FPG_IleRS	e2oq4A3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: C-terminal, Zn-finger domain of MutM-like DNA repair proteins (From Topology)	T: C-terminal, Zn-finger domain of MutM-like DNA repair proteins	F: zf-FPG_IleRS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth 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)
F [auth B]	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E [auth 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)
E [auth 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
E [auth A], F [auth B]	PF06827	Zinc finger found in FPG and IleRS (zf-FPG_IleRS)	Zinc finger found in FPG and IleRS	This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.	Domain
E [auth A], F [auth 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
E [auth A], F [auth B]	PF01149	Formamidopyrimidine-DNA glycosylase N-terminal domain (Fapy_DNA_glyco)	Formamidopyrimidine-DNA glycosylase N-terminal domain	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1 ...	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B]	Endonuclease VIII	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 oxidized base lesion DNA N-glycosylase activity hydrolase activity 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 oxidized base lesion DNA N-glycosylase activity hydrolase activity oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding 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	-
B [auth D], D [auth F]	5'-D(CCPAPGPGPAP(PED)PGPAPAPGPCP*C)-3'	-	-	-
A [auth C], C [auth E]	5'-D(GGPCPTPTPCPAPTPCPCPTPGP*G)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR000214	Zinc finger, DNA glycosylase/AP lyase-type	Domain
E [auth A], F [auth B]	IPR015887	DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site	Binding Site
E [auth A], F [auth B]	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain	Domain
E [auth A], F [auth B]	IPR015886	Formamidopyrimidine-DNA glycosylase, H2TH DNA-binding	Domain
E [auth A], F [auth B]	IPR035937	Formamidopyrimidine-DNA glycosylase, N-terminal	Homologous Superfamily
E [auth A], F [auth B]	IPR010663	Zinc finger, FPG/IleRS-type	Domain
E [auth A], F [auth B]	IPR044091	Nei, N-terminal	Domain
E [auth A], F [auth B]	IPR010979	Small ribosomal subunit protein uS13-like, H2TH	Homologous Superfamily
E [auth A], F [auth B]	IPR023713	Endonuclease VIII	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth D], D [auth F]	PED	RESID: AA0494 PSI-MOD : N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-prolinium MOD:01454

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.