3IH7

Crystal structure of catalytically active human 8-oxoguanine glycosylase distally crosslinked to guanine-containing DNA

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	TATA-box binding protein-like	8036320	3000705	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-glycosylase	8036319	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)
A	HhH-GPD	e3ih7A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD	ECOD (1.6)
A	OGG_N	e3ih7A2	A: a+b two layers	X: TBP-like	H: TATA-box binding protein-like (From Topology)	T: TATA-box binding protein-like	F: OGG_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.310.40	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein		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	PF07934	8-oxoguanine DNA glycosylase, N-terminal domain (OGG_N)	8-oxoguanine DNA glycosylase, N-terminal domain	-	Family
A	PF00730	HhH-GPD superfamily base excision DNA repair protein (HhH-GPD)	HhH-GPD superfamily base excision DNA repair protein	This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonucle ...	This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as Swiss:P53397. The methyl-CPG binding protein MBD4 Swiss:Q9Z2D7 also contains a related domain [1] that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	N-glycosylase/DNA lyase	DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid 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 DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid 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 cytoskeletal protein binding microtubule binding protein binding tubulin binding DNA-(apurinic or apyrimidinic site) endonuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity carbon-oxygen lyase activity oxidized DNA binding oxidized purine DNA binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus nucleobase-containing compound metabolic process base-excision repair organic substance metabolic process DNA modification heterocycle metabolic process nitrogen compound metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus nucleobase-containing compound metabolic process base-excision repair organic substance metabolic process DNA modification heterocycle metabolic process nitrogen compound metabolic process DNA repair cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process organic cyclic compound metabolic process depurination macromolecule modification metabolic process macromolecule metabolic process base-excision repair, AP site formation cellular aromatic compound metabolic process regulation of cellular process regulation of double-strand break repair double-strand break repair via single-strand annealing regulation of cellular response to stress negative regulation of biological process negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process negative regulation of double-strand break repair negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process negative regulation of DNA repair regulation of response to stress negative regulation of cellular process negative regulation of double-strand break repair via single-strand annealing negative regulation of macromolecule metabolic process negative regulation of response to stimulus biological regulation regulation of macromolecule metabolic process regulation of DNA repair negative regulation of DNA metabolic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death response to radiation response to abiotic stimulus response to light stimulus deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process cellular catabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process pyrimidine-containing compound metabolic process aromatic compound catabolic process nucleotide metabolic process cellular nitrogen compound catabolic process nucleobase-containing compound catabolic process heterocycle catabolic process pyrimidine deoxyribonucleotide catabolic process catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide catabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process depyrimidination nucleotide catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process 2'-deoxyribonucleotide metabolic process deoxyribose phosphate metabolic process organic cyclic compound catabolic process organophosphate metabolic process organic substance catabolic process response to organic substance response to alcohol response to oxygen-containing compound response to ethanol cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription nucleotide-excision repair response to extracellular stimulus response to nutrient levels response to organonitrogen compound response to folic acid response to nutrient response to external stimulus response to nitrogen compound response to vitamin response to organic cyclic compound response to oxidative stress cellular response to inorganic substance cellular response to metal ion response to cadmium ion response to inorganic substance cellular response to chemical stimulus response to metal ion cellular response to cadmium ion response to lipid response to estradiol	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nuclear speck membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nuclear speck nuclear body nucleoplasm cytoplasm cytosol protein-containing complex mitochondrion mitochondrial matrix
B	5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPG)-3'	-	-	-
C	5'-D(APTPCPTPGPGPAPCPCPTPGPCPA)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003265	HhH-GPD domain	Domain
A	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal	Homologous Superfamily
A	IPR011257	DNA glycosylase	Homologous Superfamily
A	IPR012904	8-oxoguanine DNA glycosylase, N-terminal	Domain
A	IPR004577	8-oxoguanine DNA-glycosylase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O15527	renal cell carcinoma Huntington disease developmental coordination disorder heart disease sarcomatoid renal cell carcinoma lymphoma brain disease chromophobe renal cell carcinoma collecting duct carcinoma Prenatal Exposure Delayed Effects prostate cancer tubular adenocarcinoma adenocarcinoma male infertility papillary renal cell carcinoma renal cell carcinoma Huntington disease developmental coordination disorder heart disease sarcomatoid renal cell carcinoma lymphoma brain disease chromophobe renal cell carcinoma collecting duct carcinoma Prenatal Exposure Delayed Effects prostate cancer tubular adenocarcinoma adenocarcinoma male infertility papillary renal cell carcinoma granular cell carcinoma hyperplasia type 2 diabetes mellitus nonpapillary renal cell carcinoma clear cell renal carcinoma primitive neuroectodermal tumor psoriasis inherited disease susceptibility tuberculosis lung benign neoplasm astrocytic tumor malignant mesothelioma medulloblastoma noise induced hearing loss obesity disorder ovarian cancer cribriform carcinoma of breast hereditary clear cell renal cell carcinoma renal carcinoma skin disease juvenile Huntington disease lung cancer breast carcinoma oligodendroglioma HIV infectious disease lung adenocarcinoma benign urinary system neoplasm maturity-onset diabetes of the young osteosarcoma cribriform carcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.