1Q57 | pdb_00001q57

The Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7

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	d1q57a1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Gene 4 protein (g4p, DNA primase), helicase domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
A	d1q57a2	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	Primase fragment of primase-helicase protein	Primase fragment of primase-helicase protein	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
B	d1q57b1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Gene 4 protein (g4p, DNA primase), helicase domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
B	d1q57b2	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	Primase fragment of primase-helicase protein	Primase fragment of primase-helicase protein	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
C	d1q57c1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Gene 4 protein (g4p, DNA primase), helicase domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
C	d1q57c2	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	Primase fragment of primase-helicase protein	Primase fragment of primase-helicase protein	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
D	d1q57d1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Gene 4 protein (g4p, DNA primase), helicase domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
D	d1q57d2	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	Primase fragment of primase-helicase protein	Primase fragment of primase-helicase protein	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
E	d1q57e1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Gene 4 protein (g4p, DNA primase), helicase domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
E	d1q57e2	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	Primase fragment of primase-helicase protein	Primase fragment of primase-helicase protein	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
F	d1q57f1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Gene 4 protein (g4p, DNA primase), helicase domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
F	d1q57f2	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	Primase fragment of primase-helicase protein	Primase fragment of primase-helicase protein	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
G	d1q57g1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Gene 4 protein (g4p, DNA primase), helicase domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
G	d1q57g2	Multi-domain proteins (alpha and beta)	DNA primase core	DNA primase core	Primase fragment of primase-helicase protein	Primase fragment of primase-helicase protein	(Escherichia phage T7 ) [TaxId: 10760 ],	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	8018199	3000737	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	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	EUF08431	e1q57A1	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: EUF08431	ECOD (1.6)
A	AAA_25	e1q57A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_25	ECOD (1.6)
A	Toprim_2	e1q57A3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
B	EUF08431	e1q57B1	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: EUF08431	ECOD (1.6)
B	AAA_25	e1q57B2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_25	ECOD (1.6)
B	Toprim_2	e1q57B3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
C	EUF08431	e1q57C1	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: EUF08431	ECOD (1.6)
C	AAA_25	e1q57C2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_25	ECOD (1.6)
C	Toprim_2	e1q57C3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
D	EUF08431	e1q57D1	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: EUF08431	ECOD (1.6)
D	AAA_25	e1q57D2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_25	ECOD (1.6)
D	Toprim_2	e1q57D3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
E	EUF08431	e1q57E1	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: EUF08431	ECOD (1.6)
E	AAA_25	e1q57E2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_25	ECOD (1.6)
E	Toprim_2	e1q57E3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
F	EUF08431	e1q57F1	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: EUF08431	ECOD (1.6)
F	AAA_25	e1q57F2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_25	ECOD (1.6)
F	Toprim_2	e1q57F3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
G	EUF08431	e1q57G1	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: EUF08431	ECOD (1.6)
G	AAA_25	e1q57G2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_25	ECOD (1.6)
G	Toprim_2	e1q57G3	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	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	2.20.25.180	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
G	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
G	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, B, C, D, E A, B, C, D, E, F, G	PF21268	Bacteriophage T7 DNA helicase/primase, N-terminal a+b fold (Helic-prim_T7_N)	Bacteriophage T7 DNA helicase/primase, N-terminal a+b fold	Bacteriophage T7 DNA helicase/primase (also known as Gp4) is an ATP-dependent DNA helicase and primase that is essential for viral DNA replication and recombination [1-4]. Primase activity synthesises short RNA primers at the sequence 5'-GTC-3' on th ...	Bacteriophage T7 DNA helicase/primase (also known as Gp4) is an ATP-dependent DNA helicase and primase that is essential for viral DNA replication and recombination [1-4]. Primase activity synthesises short RNA primers at the sequence 5'-GTC-3' on the lagging strand that the polymerase elongates using dNTPs and providing the primase is still present. It consists of an N-terminal zinc ribbon (Pfam:PF08273) followed by a RNA Polymerase Domain that can be subdivided in an N-terminal alpha+beta structure, represented in this entry and a C-terminal TOPRIM fold (Pfam:PF13155) [1]. At the C-terminal end of the protein there is a DNA helicase domain (Pfam:PF03796).	Domain
A, B, C, D, E A, B, C, D, E, F, G	PF03796	DnaB-like helicase C terminal domain (DnaB_C)	DnaB-like helicase C terminal domain	The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the q ...	The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.	Domain
A, B, C, D, E A, B, C, D, E, F, G	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, C, D, E A, B, C, D, E, F, G	DNA primase/helicase	nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity DNA translocase activity chromatin extrusion motor activity ATP-dependent H3-H4 histone complex chaperone activity nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity DNA translocase activity chromatin extrusion motor activity ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity protein carrier chaperone ATP-dependent histone chaperone activity molecular carrier activity cohesin loader activity DNA clamp loader activity ATP-dependent H2AZ histone chaperone activity forked DNA-dependent helicase 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 single-stranded DNA helicase activity 3'-5' DNA helicase activity single-stranded 3'-5' DNA helicase activity four-way junction helicase activity 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 identical protein binding protein binding DNA binding single-stranded DNA binding nucleic acid binding double-stranded DNA helicase activity	viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process metabolic process cellular process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR006171	TOPRIM domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR034154	Archaeal primase DnaG/twinkle-like, TOPRIM domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR027032	Twinkle-like protein	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR013237	DNA primase/helicase Gp4, N-terminal, Bacteriophage T7-like	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR048774	Bacteriophage T7 DNA helicase/primase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR007694	DNA helicase, DnaB-like, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR046394	Bacteriophage T7 DNA helicase/primase	Family