8G9F | pdb_00008g9f

Complete auto-inhibitory complex of Xenopus laevis DNA polymerase alpha-primase

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	F_UNCLASSIFIED	e8g9fD1	A: alpha arrays	X: Insert all-alpha domain in prim-pol (From Topology)	H: Insert all-alpha domain in prim-pol (From Topology)	T: Insert all-alpha domain in prim-pol	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e8g9fD2	A: a+b complex topology	X: Prim-pol domain (From Topology)	H: Prim-pol domain (From Topology)	T: Prim-pol domain	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8g9fC2	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Fe-S cluster domain of DNA primase	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8g9fC1	A: alpha complex topology	X: PriB N-terminal domain-like (From Topology)	H: PriB N-terminal domain-like (From Topology)	T: PriB N-terminal domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8g9fB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8g9fB2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8g9fA3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8g9fA5	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8g9fA7	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8g9fA1	A: a+b two layers	X: Alpha-beta plaits	H: Family B DNA polymerase insertion domain (From Topology)	T: Family B DNA polymerase insertion domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8g9fA6	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8g9fA4	A: few secondary structure elements	X: Rubredoxin-like	H: Zinc finger domain of DNA polymerase-alpha (From Topology)	T: Zinc finger domain of DNA polymerase-alpha	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.2820	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF01896	DNA primase small subunit (DNA_primase_S)	DNA primase small subunit	-	Family
C	PF04104	Eukaryotic and archaeal DNA primase, large subunit C-terminal domain (DNA_primase_lrg)	Eukaryotic and archaeal DNA primase, large subunit C-terminal domain	DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 ( ...	DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae) [1]. The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [4]. This entry represents the C-terminal alpha helical domain.	Domain
B	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
B	PF22062	DNA polymerase alpha subunit B, OB domain (OB_DPOA2)	DNA polymerase alpha subunit B, OB domain	This entry represents the OB domain of DNA polymerase alpha subunit B [1-4]. B subunits of DNA polymerases stabilize the catalytic subunit, play a role in regulation of the DNA synthesis in a cell cycle-dependent manner and act as scaffolds mediating ...	This entry represents the OB domain of DNA polymerase alpha subunit B [1-4]. B subunits of DNA polymerases stabilize the catalytic subunit, play a role in regulation of the DNA synthesis in a cell cycle-dependent manner and act as scaffolds mediating interactions with other components of the replication machinery [1-4].	Domain
A	PF08996	DNA Polymerase alpha zinc finger (zf-DNA_Pol)	DNA Polymerase alpha zinc finger	The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parall ...	The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain [1].	Domain
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
A	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	DNA primase	DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome
C	DNA primase large subunit	DNA binding binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome
B	DNA polymerase alpha subunit B	DNA binding binding nucleic acid binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome
A	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 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 DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process 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 cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress DNA repair	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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR002755	DNA primase, small subunit	Family
D	IPR014052	DNA primase, small subunit, eukaryotic/archaeal	Family
C	IPR016558	DNA primase, large subunit, eukaryotic	Family
C	IPR007238	DNA primase large subunit, eukaryotic/archaeal	Family
B	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
B	IPR054300	DNA polymerase alpha subunit B, OB domain	Domain
B	IPR043034	DNA polymerase alpha, subunit B, N-terminal domain superfamily	Homologous Superfamily
B	IPR013627	DNA polymerase alpha, subunit B, N-terminal	Domain
B	IPR016722	DNA polymerase alpha, subunit B	Family
A	IPR038256	DNA polymerase alpha, zinc finger domain superfamily	Homologous Superfamily
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR045846	DNA polymerase alpha catalytic subunit, catalytic domain	Domain
A	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A	IPR015088	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Domain
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A	IPR024647	DNA polymerase alpha catalytic subunit, N-terminal domain	Domain