Annotations: 4NL4

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth H]	PriA_like	e4nl4H2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PriA_like	ECOD (1.6)
A [auth H]	PRK05580_C	e4nl4H7	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein S10 (From Topology)	T: Ribosomal protein S10	F: PRK05580_C	ECOD (1.6)
A [auth H]	PRK05580_N	e4nl4H1	A: a+b complex topology	X: Primosome assembly protein PriA 3' DNA-binding domain (From Topology)	H: Primosome assembly protein PriA 3' DNA-binding domain (From Topology)	T: Primosome assembly protein PriA 3' DNA-binding domain	F: PRK05580_N	ECOD (1.6)
A [auth H]	DEAD	e4nl4H3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
A [auth H]	Helicase_C_9	e4nl4H4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_9	ECOD (1.6)
A [auth H]	PriA	e4nl4H5	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PriA	ECOD (1.6)
A [auth H]	priA	e4nl4H6	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: priA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	3.40.1440.60	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	PriA, 3(prime) DNA-binding domain	CATH (4.3.0)
A [auth H]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H]	PF18074	Primosomal protein N C-terminal domain (PriA_C)	Primosomal protein N C-terminal domain	This is the C-terminal domain found in PriA DNA helicase, a multifunctional enzyme that mediates the process of restarting prematurely terminated DNA replication reactions in bacteria. The C-terminal domain (CTD) bears similarity to the S10 subunit w ...	This is the C-terminal domain found in PriA DNA helicase, a multifunctional enzyme that mediates the process of restarting prematurely terminated DNA replication reactions in bacteria. The C-terminal domain (CTD) bears similarity to the S10 subunit which binds branched rRNA within the bacterial ribosome. The C-terminal domain is part of the helicase domain of PriA proteins. It acts together with the 3' DNA-binding domain to form a site for binding ssDNA-binding protein (SSB) [1].	Domain
A [auth H]	PF21213	Primosomal protein N'-like, winged helix (PriA-like_WH)	Primosomal protein N'-like, winged helix	This domain is found in Primosomal protein N' from Escherichia coli (PriA) and similar proteins predominantly found in Proteobacteria. PriA is a DNA helicase involved in the restart of stalled replication forks, which are lethal in bacteria if left ...	This domain is found in Primosomal protein N' from Escherichia coli (PriA) and similar proteins predominantly found in Proteobacteria. PriA is a DNA helicase involved in the restart of stalled replication forks, which are lethal in bacteria if left unrepaired. This protein shows a modular arrangement in which its central helicase core is surrounded by several DNA-binding elements, including a circularly permuted winged helix (WH) domain (this entry), which is located towards the N-terminal of the protein and can bind DNA in isolation [1,2].	Domain
A [auth H]	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A [auth H]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A [auth H]	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
A [auth H]	PF18319	PriA DNA helicase Cys-rich region (CRR) domain (PriA_CRR)	PriA DNA helicase Cys-rich region (CRR) domain	This is a cys-rich region (CRR) domain found in PriA DNA helicases. In bacteria, the replication restart process is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with for ...	This is a cys-rich region (CRR) domain found in PriA DNA helicases. In bacteria, the replication restart process is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). The CRR region which is embedded within the C-terminal helicase lobe has been identified to bind two Zn2+ ions. This 50-residue insertion forms a structure on the surface of the helicase core in which two Zn2+ ions are coordinated by invariant Cys residues. Biochemical experiments have shown that sequence changes to Zn2+-binding Cys residues in the PriA CRR can eliminate helicase, but not ATPase, activity and can block assembly of PriB onto DNA-bound PriA, implicating the CRR in multiple functions in PriA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	Primosome assembly protein PriA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding metal ion binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity	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 organic cyclic compound metabolic process nucleic acid biosynthetic process DNA replication 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 organic cyclic compound metabolic process nucleic acid biosynthetic process DNA replication organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic 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	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth H]	IPR041222	Primosomal protein N', 3' DNA-binding domain	Domain
A [auth H]	IPR042115	Primosomal protein N', 3' DNA-binding domain superfamily	Homologous Superfamily
A [auth H]	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth H]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth H]	IPR048949	Primosomal protein N'-like, winged helix	Domain
A [auth H]	IPR041236	Primosomal protein N, C-terminal domain	Domain
A [auth H]	IPR005259	Primosomal protein N'	Family
A [auth H]	IPR040498	PriA DNA helicase, Cys-rich region (CRR) domain	Domain
A [auth H]	IPR011545	DEAD/DEAH box helicase domain	Domain
A [auth H]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.