5W35

Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with a double-stranded DNA oligomer with a 1-nucleotide overhang

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)
A	DnaB_bind	e5w35A3	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	e5w35A2	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	e5w35A1	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	e5w35B1	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	e5w35B2	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	e5w35B3	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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 cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process DNA-templated DNA replication cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process cellular process macromolecule metabolic process	primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle cell periphery plasma membrane primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle cell periphery plasma membrane membrane cytoplasm transferase complex, transferring phosphorus-containing groups catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
C	synthetic DNA oligomer 5'-CCACTTCCGGTC	-	-	-
D	synthetic DNA oligomer 5'-TGACCGGAAGTGG	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013173	DNA primase DnaG, DnaB-binding domain	Domain
A, B	IPR037068	DNA primase, catalytic core, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR034151	Bacterial DnaG primase, TOPRIM domain	Domain
A, B	IPR030846	DNA primase DnaG, bacteria	Family
A, B	IPR006295	DNA primase, DnaG	Domain
A, B	IPR006171	TOPRIM domain	Domain
A, B	IPR002694	Zinc finger, CHC2-type	Domain
A, B	IPR036977	DNA Primase, CHC2-type zinc finger	Homologous Superfamily
A, B	IPR013264	DNA primase DNAG, catalytic core, N-terminal	Domain
A, B	IPR050219	DnaG Primase	Family
A, B	IPR019475	DNA primase, DnaB-helicase binding domain	Domain

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.