1EQN

E.COLI PRIMASE CATALYTIC CORE

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1eqna_	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	DNA primase DnaG catalytic core	DNA primase DnaG catalytic core	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1eqnb_	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	DNA primase DnaG catalytic core	DNA primase DnaG catalytic core	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1eqnc_	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	DNA primase DnaG catalytic core	DNA primase DnaG catalytic core	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1eqnd_	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	DNA primase DnaG catalytic core	DNA primase DnaG catalytic core	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1eqne_	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	DNA primase DnaG catalytic core	DNA primase DnaG catalytic core	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Toprim domain-like	8037559	3000737	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Toprim domain-like	8037559	3000737	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Toprim domain-like	8037559	3000737	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Toprim domain-like	8037559	3000737	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Toprim domain-like	8037559	3000737	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	DnaB_bind	e1eqnA3	A: alpha bundles	X: helical domain in DNA primase DnaG catalytic core (From Topology)	H: helical domain in DNA primase DnaG catalytic core (From Topology)	T: helical domain in DNA primase DnaG catalytic core	F: DnaB_bind	ECOD (1.6)
A	Toprim_N	e1eqnA1	A: a+b two layers	X: N-terminal a+b domain in DNA primase core (From Topology)	H: N-terminal a+b domain in DNA primase core (From Topology)	T: N-terminal a+b domain in DNA primase core	F: Toprim_N	ECOD (1.6)
A	Toprim_2	e1eqnA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
B	DnaB_bind	e1eqnB3	A: alpha bundles	X: helical domain in DNA primase DnaG catalytic core (From Topology)	H: helical domain in DNA primase DnaG catalytic core (From Topology)	T: helical domain in DNA primase DnaG catalytic core	F: DnaB_bind	ECOD (1.6)
B	Toprim_N	e1eqnB1	A: a+b two layers	X: N-terminal a+b domain in DNA primase core (From Topology)	H: N-terminal a+b domain in DNA primase core (From Topology)	T: N-terminal a+b domain in DNA primase core	F: Toprim_N	ECOD (1.6)
B	Toprim_2	e1eqnB2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
C	DnaB_bind	e1eqnC3	A: alpha bundles	X: helical domain in DNA primase DnaG catalytic core (From Topology)	H: helical domain in DNA primase DnaG catalytic core (From Topology)	T: helical domain in DNA primase DnaG catalytic core	F: DnaB_bind	ECOD (1.6)
C	Toprim_N	e1eqnC1	A: a+b two layers	X: N-terminal a+b domain in DNA primase core (From Topology)	H: N-terminal a+b domain in DNA primase core (From Topology)	T: N-terminal a+b domain in DNA primase core	F: Toprim_N	ECOD (1.6)
C	Toprim_2	e1eqnC2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
D	DnaB_bind	e1eqnD3	A: alpha bundles	X: helical domain in DNA primase DnaG catalytic core (From Topology)	H: helical domain in DNA primase DnaG catalytic core (From Topology)	T: helical domain in DNA primase DnaG catalytic core	F: DnaB_bind	ECOD (1.6)
D	Toprim_N	e1eqnD1	A: a+b two layers	X: N-terminal a+b domain in DNA primase core (From Topology)	H: N-terminal a+b domain in DNA primase core (From Topology)	T: N-terminal a+b domain in DNA primase core	F: Toprim_N	ECOD (1.6)
D	Toprim_2	e1eqnD2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
E	DnaB_bind	e1eqnE3	A: alpha bundles	X: helical domain in DNA primase DnaG catalytic core (From Topology)	H: helical domain in DNA primase DnaG catalytic core (From Topology)	T: helical domain in DNA primase DnaG catalytic core	F: DnaB_bind	ECOD (1.6)
E	Toprim_N	e1eqnE1	A: a+b two layers	X: N-terminal a+b domain in DNA primase core (From Topology)	H: N-terminal a+b domain in DNA primase core (From Topology)	T: N-terminal a+b domain in DNA primase core	F: Toprim_N	ECOD (1.6)
E	Toprim_2	e1eqnE2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.980.10	Alpha Beta	Alpha-Beta Complex	DNA primase DNAg catalytic core, N-terminal domain	DNA primase, catalytic core, N-terminal domain	CATH (4.3.0)
A	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
A	1.20.50.20	Mainly Alpha	Up-down Bundle	Pheromone ER-1	DnaG, RNA polymerase domain, helical bundle	CATH (4.3.0)
B	3.90.980.10	Alpha Beta	Alpha-Beta Complex	DNA primase DNAg catalytic core, N-terminal domain	DNA primase, catalytic core, N-terminal domain	CATH (4.3.0)
B	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
B	1.20.50.20	Mainly Alpha	Up-down Bundle	Pheromone ER-1	DnaG, RNA polymerase domain, helical bundle	CATH (4.3.0)
C	3.90.980.10	Alpha Beta	Alpha-Beta Complex	DNA primase DNAg catalytic core, N-terminal domain	DNA primase, catalytic core, N-terminal domain	CATH (4.3.0)
C	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
C	1.20.50.20	Mainly Alpha	Up-down Bundle	Pheromone ER-1	DnaG, RNA polymerase domain, helical bundle	CATH (4.3.0)
D	3.90.980.10	Alpha Beta	Alpha-Beta Complex	DNA primase DNAg catalytic core, N-terminal domain	DNA primase, catalytic core, N-terminal domain	CATH (4.3.0)
D	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
D	1.20.50.20	Mainly Alpha	Up-down Bundle	Pheromone ER-1	DnaG, RNA polymerase domain, helical bundle	CATH (4.3.0)
E	3.90.980.10	Alpha Beta	Alpha-Beta Complex	DNA primase DNAg catalytic core, N-terminal domain	DNA primase, catalytic core, N-terminal domain	CATH (4.3.0)
E	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
E	1.20.50.20	Mainly Alpha	Up-down Bundle	Pheromone ER-1	DnaG, RNA polymerase domain, helical bundle	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF10410	DnaB-helicase binding domain of primase (DnaB_bind)	DnaB-helicase binding domain of primase	This domain is the C-terminal region three-helical domain of primase [1]. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Pri ...	This domain is the C-terminal region three-helical domain of primase [1]. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase [2]. It is associated with the Toprim domain (Pfam:PF01751) which is the central catalytic core.	Domain
A, B, C, D, E	PF08275	DNA primase catalytic core, N-terminal domain (DNAG_N)	DNA primase catalytic core, N-terminal domain	DNA primase (DNAG) is a a nucleotidyltransferase which synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell divisi ...	DNA primase (DNAG) is a a nucleotidyltransferase which synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division [1]. Primases comprise three domains: a zinc-binding domain at the N-terminal (Pfam:PF01807), a polymerase domain (catalytic core), and a domain that interacts with the replicative helicase (Pfam:PF01807). The catalytic core consists of an alpha+beta domain at the N-terminal (this entry) and a TOPRIM domain at the C-terminal (Pfam:PF13155) [1,2].	Domain
A, B, C, D, E	PF13155	Toprim-like (Toprim_2)	Toprim-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	DNA PRIMASE	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity DNA primase 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 DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity DNA primase 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 transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process replication fork processing cellular biosynthetic process DNA replication, synthesis of primer DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process replication fork processing cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process cellular process DNA duplex unwinding DNA geometric change chromosome organization DNA conformation change DNA unwinding involved in DNA replication cellular component organization organelle organization cellular component organization or biogenesis	protein-containing complex primosome complex intracellular anatomical structure catalytic complex protein-DNA complex chromosome cellular anatomical entity intracellular organelle core primosome complex DnaB-DnaG complex organelle intracellular non-membrane-bounded organelle replication fork DNA helicase complex protein-containing complex primosome complex intracellular anatomical structure catalytic complex protein-DNA complex chromosome cellular anatomical entity intracellular organelle core primosome complex DnaB-DnaG complex organelle intracellular non-membrane-bounded organelle replication fork DNA helicase complex replisome non-membrane-bounded organelle cytoplasm transferase complex, transferring phosphorus-containing groups RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR013173	DNA primase DnaG, DnaB-binding domain	Domain
A, B, C, D, E	IPR037068	DNA primase, catalytic core, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR016136	DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal	Homologous Superfamily
A, B, C, D, E	IPR034151	Bacterial DnaG primase, TOPRIM domain	Domain
A, B, C, D, E	IPR030846	DNA primase DnaG, bacteria	Family
A, B, C, D, E	IPR006295	DNA primase, DnaG	Domain
A, B, C, D, E	IPR006171	TOPRIM domain	Domain
A, B, C, D, E	IPR002694	Zinc finger, CHC2-type	Domain
A, B, C, D, E	IPR036977	DNA Primase, CHC2-type zinc finger	Homologous Superfamily
A, B, C, D, E	IPR013264	DNA primase DNAG, catalytic core, N-terminal	Domain
A, B, C, D, E	IPR019475	DNA primase, DnaB-helicase binding domain	Domain

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.