6N9V | pdb_00006n9v

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS1)

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8018194	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	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 [auth H]	SCOP2B Superfamily	Ribonuclease H-like	8040253	3000143	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8040254	3001272	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	AAA_25	e6n9vA1	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	AAA_25	e6n9vB1	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	AAA_25	e6n9vC1	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	AAA_25	e6n9vD1	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	EUF08431	e6n9vE1	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	e6n9vE3	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	e6n9vE2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
E	Prim_Zn_Ribbon	e6n9vE4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Prim_Zn_Ribbon	ECOD (1.6)
F	EUF08431	e6n9vF3	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	e6n9vF2	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	e6n9vF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_2	ECOD (1.6)
G [auth H]	DNA_pol_A_2nd	e6n9vH3	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: DNA_pol_A_2nd	ECOD (1.6)
G [auth H]	DNA_pol_A_1st	e6n9vH2	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: DNA_pol_A_1st	ECOD (1.6)
G [auth H]	DNA_pol_A_3rd	e6n9vH1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: DNA_pol_A_3rd	ECOD (1.6)
G [auth H]	RNase_H_2	e6n9vH4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_H_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 (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
G [auth H]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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	PF08273	Zinc-binding domain of primase-helicase (Zn_Ribbon_Prim)	Zinc-binding domain of primase-helicase		Domain
A, B, C, D, E A, B, C, D, E, F	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	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	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	-
G [auth H]	DNA-directed DNA polymerase	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA exonuclease activity DNA nuclease activity cation binding ion binding metal ion binding	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 DNA synthesis involved in DNA replication DNA replication DNA-templated DNA replication cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair	-
H [auth P]	Primer	-	-	-
I [auth T]	Template	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006171	TOPRIM domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR034154	Archaeal primase DnaG/twinkle-like, TOPRIM domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027032	Twinkle-like protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR013237	DNA primase/helicase Gp4, N-terminal, Bacteriophage T7-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR048774	Bacteriophage T7 DNA helicase/primase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR007694	DNA helicase, DnaB-like, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046394	Bacteriophage T7 DNA helicase/primase	Family
G [auth H]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
G [auth H]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
G [auth H]	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
G [auth H]	IPR034699	DNA-directed DNA polymerase T7	Family
G [auth H]	IPR002298	DNA polymerase A	Family
G [auth H]	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
G [auth H]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

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.