4IEM

Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+

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	DNase I-like	8036725	3000957	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	DNase I-like	8036725	3000957	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	DNase I-like	8036725	3000957	SCOP2B (2022-06-29)
M [auth D]	SCOP2B Superfamily	DNase I-like	8036725	3000957	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	Exo_endo_phos	e4iemA1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
E [auth B]	Exo_endo_phos	e4iemB2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
I [auth C]	Exo_endo_phos	e4iemC2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
M [auth D]	Exo_endo_phos	e4iemD2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
E [auth B]	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
I [auth C]	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
M [auth D]	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth B], I [auth C], M [auth D]	PF03372	Endonuclease/Exonuclease/phosphatase family (Exo_endo_phos)	Endonuclease/Exonuclease/phosphatase family	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3. ...	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth B], I [auth C], M [auth D]	DNA-(apurinic or apyrimidinic site) lyase	DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid endodeoxyribonuclease activity, producing 5'-phosphomonoesters hydrolase activity DNA nuclease activity DNA endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity class II DNA-(apurinic or apyrimidinic site) endonuclease activity site-specific endodeoxyribonuclease activity, specific for altered base DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid endodeoxyribonuclease activity, producing 5'-phosphomonoesters hydrolase activity DNA nuclease activity DNA endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity class II DNA-(apurinic or apyrimidinic site) endonuclease activity site-specific endodeoxyribonuclease activity, specific for altered base phosphoric ester hydrolase activity phosphodiesterase I activity phosphoric diester hydrolase activity exonuclease activity double-stranded DNA 3'-5' DNA exonuclease activity DNA exonuclease activity 3'-5' exonuclease activity double-stranded DNA exodeoxyribonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 3'-5'-DNA exonuclease activity DNA binding binding organic cyclic compound binding nucleic acid binding damaged DNA binding DNA-(abasic site) binding cation binding ion binding metal ion binding small molecule binding oxidoreductase activity uracil DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds deaminated base DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding sequence-specific DNA binding double-stranded telomeric DNA binding double-stranded DNA binding telomeric DNA binding transcription corepressor activity phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands chromatin binding chromatin DNA binding RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity RNA endonuclease activity	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus telomere maintenance in response to DNA damage catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus telomere organization chromosome organization telomere maintenance cellular component organization organelle organization base-excision repair cellular response to stress DNA damage response response to stress cellular component organization or biogenesis telomere maintenance via base-excision repair DNA repair regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation apoptotic process regulation of programmed cell death cell death programmed cell death 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 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 positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression regulation of macromolecule metabolic process 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 regulation of metabolic process cell redox homeostasis cellular homeostasis homeostatic process positive regulation of DNA-templated transcription regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process 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 regulation of DNA-templated transcription negative regulation of biological process post-transcriptional regulation of gene expression regulation of mRNA catabolic process negative regulation of cellular process regulation of biological quality RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process negative regulation of metabolic process regulation of catabolic process mRNA metabolic process regulation of mRNA stability negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of RNA stability regulation of mRNA metabolic process DNA recombination base-excision repair, gap-filling	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm perinuclear region of cytoplasm membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region mitochondrion nucleolus centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton ribosome endoplasmic reticulum endomembrane system
B [auth E], F [auth H], J [auth K], N	DNA (5'-D(GPCPTPAP*C)-3')	-	-	-
C [auth F], G [auth I], K [auth L], O	DNA (5'-D(P(3DR)PGPAPTPCPG)-3')	-	-	-
D [auth G], H [auth J], L [auth M], P	DNA (5'-D(CPGPAPTPCPGPGPTPAPGP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth B], I [auth C], M [auth D]	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
A, E [auth B], I [auth C], M [auth D]	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A, E [auth B], I [auth C], M [auth D]	IPR020847	AP endonuclease 1, binding site	Binding Site
A, E [auth B], I [auth C], M [auth D]	IPR020848	AP endonuclease 1, conserved site	Conserved Site
A, E [auth B], I [auth C], M [auth D]	IPR004808	AP endonuclease 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, E [auth B], I [auth C], M [auth D]	Pharos: P27695	melanoma lung adenocarcinoma heart disease visual epilepsy prostate cancer Generalized Absence Seizures Takayasu arteritis hereditary diffuse gastric adenocarcinoma cutaneous melanoma ovarian cancer gastric cancer inherited disease susceptibility large cell medulloblastoma lung cancer atypical teratoid rhabdoid tumor melanoma lung adenocarcinoma heart disease visual epilepsy prostate cancer Generalized Absence Seizures Takayasu arteritis hereditary diffuse gastric adenocarcinoma cutaneous melanoma ovarian cancer gastric cancer inherited disease susceptibility large cell medulloblastoma lung cancer atypical teratoid rhabdoid tumor medulloblastoma brain injury plasma cell myeloma gastric neoplasm glioblastoma hepatocellular carcinoma astrocytic tumor lymphoplasmacytic lymphoma oligodendroglioma

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.