2DWM | pdb_00002dwm

Crystal structure of the PriA protein complexed with oligonucleotides

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)
G [auth D]	PriA_3primeBD	e2dwmD1	A: a/b three-layered sandwiches	X: Primosome assembly protein PriA 3' DNA-binding domain	H: Primosome assembly protein PriA 3' DNA-binding domain	T: Primosome assembly protein PriA 3' DNA-binding domain	F: PriA_3primeBD	ECOD (v294.1)
F [auth C]	PriA_3primeBD	e2dwmC1	A: a/b three-layered sandwiches	X: Primosome assembly protein PriA 3' DNA-binding domain	H: Primosome assembly protein PriA 3' DNA-binding domain	T: Primosome assembly protein PriA 3' DNA-binding domain	F: PriA_3primeBD	ECOD (v294.1)
E [auth B]	PriA_3primeBD	e2dwmB1	A: a/b three-layered sandwiches	X: Primosome assembly protein PriA 3' DNA-binding domain	H: Primosome assembly protein PriA 3' DNA-binding domain	T: Primosome assembly protein PriA 3' DNA-binding domain	F: PriA_3primeBD	ECOD (v294.1)
D [auth A]	PriA_3primeBD	e2dwmA1	A: a/b three-layered sandwiches	X: Primosome assembly protein PriA 3' DNA-binding domain	H: Primosome assembly protein PriA 3' DNA-binding domain	T: Primosome assembly protein PriA 3' DNA-binding domain	F: PriA_3primeBD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth D]	3.40.1440.60	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	PriA, 3(prime) DNA-binding domain	CATH (4.3.0)
F [auth C]	3.40.1440.60	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	PriA, 3(prime) DNA-binding domain	CATH (4.3.0)
E [auth B]	3.40.1440.60	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	PriA, 3(prime) DNA-binding domain	CATH (4.3.0)
D [auth A]	3.40.1440.60	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	PriA, 3(prime) DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], E [auth B], F [auth C], G [auth D]	PF17764	3'DNA-binding domain (3'BD) (PriA_3primeBD)	3'DNA-binding domain (3'BD)	This domain represents the N-terminal DNA-binding domain found in the PriA protein. The 3'BD, which has been shown to bind the 3' end of the leading-strand arm of replication fork structures.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth A], E [auth B], F [auth C], G [auth D]	Primosomal protein N	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity 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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides cation binding transition metal ion binding zinc ion binding metal ion binding DNA helicase activity 3'-5' DNA helicase activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA	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 DNA replication initiation DNA-templated DNA replication maintenance of fidelity replication fork processing response to stimulus response to chemical 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 DNA replication initiation DNA-templated DNA replication maintenance of fidelity replication fork processing response to stimulus response to chemical response to antibiotic 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 DNA recombination response to ionizing radiation response to radiation response to abiotic stimulus response to gamma radiation plasmid maintenance cellular response to stimulus double-strand break repair cellular response to stress DNA damage response response to stress DNA repair	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 DnaB-DnaC-DnaT-PriA-PriC complex pre-primosome complex 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 DnaB-DnaC-DnaT-PriA-PriC complex pre-primosome complex DnaB-DnaC-DnaT-PriA-PriB complex
A [auth E], B [auth F], C [auth G]	5'-D(APT)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], E [auth B], F [auth C], G [auth D]	IPR041222	Primosomal protein N', 3' DNA-binding domain	Domain
D [auth A], E [auth B], F [auth C], G [auth D]	IPR042115	Primosomal protein N', 3' DNA-binding domain superfamily	Homologous Superfamily
D [auth A], E [auth B], F [auth C], G [auth D]	IPR048949	Primosomal protein N'-like, winged helix	Domain
D [auth A], E [auth B], F [auth C], G [auth D]	IPR011545	DEAD/DEAH-box helicase domain	Domain
D [auth A], E [auth B], F [auth C], G [auth D]	IPR005259	Primosomal protein N'	Family
D [auth A], E [auth B], F [auth C], G [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D [auth A], E [auth B], F [auth C], G [auth D]	IPR001650	Helicase, C-terminal domain-like	Domain
D [auth A], E [auth B], F [auth C], G [auth D]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
D [auth A], E [auth B], F [auth C], G [auth D]	IPR041236	Primosomal protein N, C-terminal domain	Domain
D [auth A], E [auth B], F [auth C], G [auth D]	IPR040498	PriA DNA helicase, Cys-rich region (CRR) 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.