4EDK | pdb_00004edk

The structure of the S. aureus DnaG RNA Polymerase Domain bound to GTP and Manganese

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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_like	e4edkA4	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_like	ECOD (1.6)
A	Toprim_N	e4edkA2	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	e4edkA3	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 (4.2.0)
A	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.2.0)
A	1.20.50.20	Mainly Alpha	Up-down Bundle	Pheromone ER-1	DnaG, RNA polymerase domain, helical bundle	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA primase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding 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 transition metal ion binding zinc ion binding metal ion binding ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA helicase activity macromolecular conformation isomerase activity ATP-dependent activity	DNA-templated DNA replication DNA replication, synthesis of primer 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 DNA-templated DNA replication DNA replication, synthesis of primer 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 intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome cytoplasm transferase complex, transferring phosphorus-containing groups primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome cytoplasm transferase complex, transferring phosphorus-containing groups catalytic complex 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	IPR037068	DNA primase, catalytic core, N-terminal domain superfamily	Homologous Superfamily
A	IPR016136	DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal	Homologous Superfamily
A	IPR034151	Bacterial DnaG primase, TOPRIM domain	Domain
A	IPR030846	DNA primase DnaG, bacteria	Family
A	IPR006295	DNA primase, DnaG	Domain
A	IPR007693	DNA helicase, DnaB-like, N-terminal	Domain
A	IPR048453	DNA primase DnaG, catalytic core, helical bundle	Domain
A	IPR006171	TOPRIM domain	Domain
A	IPR002694	Zinc finger, CHC2-type	Domain
A	IPR036977	DNA Primase, CHC2-type zinc finger	Homologous Superfamily
A	IPR013264	DNA primase DNAG, catalytic core, N-terminal	Domain
A	IPR036185	DNA helicase, DnaB-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR050219	DnaG Primase	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.