1YQM

Catalytically inactive human 8-oxoguanine glycosylase crosslinked to 7-deazaguanine containing DNA

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1yqma1	All alpha proteins	DNA-glycosylase	DNA-glycosylase	DNA repair glycosylase, 2 C-terminal domains	8-oxoguanine glycosylase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d1yqma2	Alpha and beta proteins (a+b)	TBP-like	TATA-box binding protein-like	DNA repair glycosylase, N-terminal domain	8-oxoguanine glycosylase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d1yqma3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	TATA-box binding protein-like	8036320	3000705	SCOP2B (2022-06-29)
C [auth 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)
C [auth A]	HhH-GPD	e1yqmA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD	ECOD (1.6)
C [auth A]	OGG_N	e1yqmA2	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)
C [auth A]	3.30.310.40	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein		CATH (4.3.0)
C [auth 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)
C [auth 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
C [auth A]	PF07934	8-oxoguanine DNA glycosylase, N-terminal domain (OGG_N)	8-oxoguanine DNA glycosylase, N-terminal domain	-	Family
C [auth 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 [auth B]	5'-D(PGPGPTPAPGPAPCPCPTPGPGPAP*C)-3'	-	-	-
B [auth C]	5'-D(PGPTPCPCPAP(7GU)PGPTPCPTPAPC)-3'	-	-	-
C [auth A]	N-glycosylase/DNA lyase	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding damaged DNA binding hydrolase activity, acting on glycosyl bonds DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding damaged DNA 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 enzyme binding	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 primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair DNA modification 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 primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair DNA modification depurination macromolecule modification metabolic process macromolecule metabolic process base-excision repair, AP site formation DNA repair 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 regulation of primary metabolic process negative regulation of DNA repair regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via single-strand annealing regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of DNA repair regulation of response to stimulus negative regulation of DNA metabolic process regulation of metabolic process 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 pyrimidine deoxyribonucleotide catabolic process deoxyribonucleotide catabolic process catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process pyrimidine nucleotide catabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process depyrimidination nucleotide catabolic process nucleoside phosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process nucleotide metabolic process deoxyribose phosphate metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process positive regulation of biological process RNA metabolic process positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process response to alcohol response to oxygen-containing compound response to ethanol regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular response to oxidative stress cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus nucleotide-excision repair response to nutrient levels response to folic acid response to nutrient response to nitrogen compound response to vitamin response to organic cyclic compound cellular response to metal ion response to metal ion cellular response to cadmium ion response to cadmium ion positive regulation of DNA-templated transcription regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process response to lipid response to estradiol	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen nuclear matrix nuclear speck nuclear body nucleoplasm cytosol protein-containing complex mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR003265	HhH-GPD domain	Domain
C [auth A]	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal	Homologous Superfamily
C [auth A]	IPR011257	DNA glycosylase	Homologous Superfamily
C [auth A]	IPR052054	Oxidative DNA damage repair enzyme	Family
C [auth A]	IPR012904	8-oxoguanine DNA glycosylase, N-terminal	Domain
C [auth A]	IPR004577	8-oxoguanine DNA-glycosylase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth 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 malignant mesothelioma astrocytic tumor 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 maturity-onset diabetes of the young benign urinary system neoplasm osteosarcoma cribriform carcinoma

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.