9MJ5 | pdb_00009mj5

Catalytic domain of human DNA polymerase alpha in complex with DNA and RPA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8003017	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8035991	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8035663	3000135	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth S]	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
E [auth S]	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
C	PF08646	Replication factor-A C terminal domain (Rep_fac-A_C)	Replication factor-A C terminal domain	This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA [1].	Domain
B	PF08784	Replication protein A C terminal (RPA_C)	Replication protein A C terminal	This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoi ...	This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.	Domain
A	PF08661	Replication factor A protein 3 (Rep_fac-A_3)	Replication factor A protein 3	Replication factor A is involved in eukaryotic DNA replication, recombination and repair.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth T]	DNA template (35-mer)	-	-	-
E [auth S]	DNA polymerase alpha catalytic subunit	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding single-stranded DNA binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation leading strand elongation nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation leading strand elongation regulation of biosynthetic process multicellular organismal process regulation of biological process regulation of cellular process type I interferon production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process cytokine production regulation of cytokine production regulation of macromolecule biosynthetic process regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair mitotic DNA replication cell cycle DNA replication initiation nuclear DNA replication cell cycle DNA replication mitotic DNA replication initiation mitotic cell cycle nuclear cell cycle DNA replication initiation mitotic cell cycle process cell cycle cell cycle process DNA synthesis involved in DNA repair DNA biosynthetic process double-strand break repair double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membraneless organelle organelle envelope nuclear envelope endomembrane system cytoplasm cytosol nucleoplasm chromatin chromosome protein-containing complex alpha DNA polymerase:primase complex nuclear protein-containing complex nuclear chromosome transferase complex nuclear replisome replication fork catalytic complex protein-DNA complex nuclear replication fork DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex replisome
D [auth P]	RNA-DNA primer (11-mer)	-	-	-
C	Replication protein A 70 kDa DNA-binding subunit	chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding DNA binding damaged DNA binding nucleic acid binding sequence-specific DNA binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding telomeric DNA binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding DNA binding damaged DNA binding nucleic acid binding sequence-specific DNA binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding telomeric DNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process localization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process localization protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization telomere maintenance via telomerase telomere organization chromosome organization nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening telomere maintenance cellular component organization nucleic acid biosynthetic process organelle organization biosynthetic process cellular component organization or biogenesis DNA biosynthetic process multicellular organismal process multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells mismatch repair DNA repair DNA-templated DNA replication protein localization to site of double-strand break developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development DNA recombination multicellular organism development embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process double-strand break repair recombinational repair double-strand break repair via homologous recombination base-excision repair nucleotide-excision repair sexual reproduction reproductive process meiotic cell cycle cell cycle	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork DNA replication factor A complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome nucleoplasm condensed nuclear chromosome lateral element synaptonemal structure synaptonemal complex condensed chromosome male germ cell nucleus germ cell nucleus site of double-strand break site of DNA damage chromosome, telomeric region chromosomal region nuclear body PML body
B	Replication protein A 32 kDa subunit	sequence-specific DNA binding DNA binding binding nucleic acid binding telomeric DNA binding damaged DNA binding protein phosphatase binding phosphatase binding protein binding enzyme binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding sequence-specific DNA binding DNA binding binding nucleic acid binding telomeric DNA binding damaged DNA binding protein phosphatase binding phosphatase binding protein binding enzyme binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress regulation of primary metabolic process cellular response to stress response to stress regulation of response to stress recombinational repair regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination DNA repair double-strand break repair regulation of biological process DNA recombination biological regulation regulation of macromolecule metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination DNA damage response regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process localization protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization mismatch repair regulation of cell cycle phase transition DNA damage checkpoint signaling signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition regulation of signal transduction regulation of cell cycle checkpoint regulation of intracellular signal transduction regulation of signaling regulation of cell communication regulation of DNA damage checkpoint telomere organization chromosome organization telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis base-excision repair nucleotide-excision repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork DNA replication factor A complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome nucleoplasm chromatin nuclear body chromosome, telomeric region chromosomal region PML body
A	Replication protein A 14 kDa subunit	DNA binding binding damaged DNA binding nucleic acid binding single-stranded DNA binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cell cycle regulation of cell cycle nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cell cycle regulation of cell cycle mitotic cell cycle cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair base-excision repair mismatch repair cell population proliferation regulation of cell population proliferation nucleotide-excision repair telomere organization chromosome organization telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork DNA replication factor A complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome site of double-strand break site of DNA damage nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth S]	IPR038256	DNA polymerase alpha, zinc finger domain superfamily	Homologous Superfamily
E [auth S]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
E [auth S]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
E [auth S]	IPR045846	DNA polymerase alpha catalytic subunit, catalytic domain	Domain
E [auth S]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
E [auth S]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
E [auth S]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
E [auth S]	IPR015088	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Domain
E [auth S]	IPR006172	DNA-directed DNA polymerase, family B	Family
E [auth S]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
E [auth S]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
E [auth S]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
E [auth S]	IPR024647	DNA polymerase alpha catalytic subunit, N-terminal domain	Domain
C	IPR007199	Replication factor-A protein 1, N-terminal	Domain
C	IPR047192	Replication factor A, C-terminal, eukaryotes	Domain
C	IPR013955	Replication factor A, C-terminal	Domain
C	IPR031657	Replication protein A, OB domain	Domain
C	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C	IPR004591	Replication factor A protein 1	Family
B	IPR014892	Replication protein A, C-terminal	Domain
B	IPR040260	Replication factor A protein-like	Family
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR014646	Replication factor A protein 2	Family
B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR013970	Replication factor A protein 3	Family
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth S]	Pharos: P09884	X-linked reticulate pigmentary disorder ovarian cancer PIGMENTARY DISORDER, RETICULATE, WITH SYSTEMIC MANIFESTATIONS acute lymphoblastic leukemia atypical teratoid rhabdoid tumor intellectual disability malignant mesothelioma neurofibromatosis type 1 pancreatic adenocarcinoma primitive neuroectodermal tumor acute myeloid leukemia B-cell chronic lymphocytic leukemia large cell medulloblastoma malignant colon neoplasm mantle cell lymphoma X-linked reticulate pigmentary disorder ovarian cancer PIGMENTARY DISORDER, RETICULATE, WITH SYSTEMIC MANIFESTATIONS acute lymphoblastic leukemia atypical teratoid rhabdoid tumor intellectual disability malignant mesothelioma neurofibromatosis type 1 pancreatic adenocarcinoma primitive neuroectodermal tumor acute myeloid leukemia B-cell chronic lymphocytic leukemia large cell medulloblastoma malignant colon neoplasm mantle cell lymphoma non-small cell lung carcinoma tuberculosis acute promyelocytic leukemia glioblastoma malignant glioma medulloblastoma N syndrome
C	Pharos: P27694	Chloracne astrocytic tumor breast cancer glioblastoma malignant ependymoma ovarian cancer atypical teratoid rhabdoid tumor Hodgkins lymphoma malignant mesothelioma psoriasis B-cell chronic lymphocytic leukemia dermatomyositis lymphoplasmacytic lymphoma medulloblastoma
B	Pharos: P15927	diabetes mellitus lymphoplasmacytic lymphoma ovarian cancer
A	Pharos: P35244	breast cancer ovarian cancer lung cancer pancreatic intraductal papillary-mucinous neoplasm malignant mesothelioma Stevens-Johnson syndrome