6N9U

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with primase domains of two gp4 subunits bound to an RNA/DNA hybrid and dTTP (from LagS1)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth E]	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
B [auth F]	SCOP2B Superfamily	Toprim domain-like	8018199	3000737	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8040254	3001272	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Ribonuclease H-like	8040253	3000143	SCOP2B (2022-06-29)
C [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 [auth E]	PF21268	e6n9uE2	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: PF21268	ECOD (1.6)
A [auth E]	PF13155	e6n9uE3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PF13155	ECOD (1.6)
A [auth E]	PF08273	e6n9uE1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF08273	ECOD (1.6)
B [auth F]	PF21268	e6n9uF2	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: PF21268	ECOD (1.6)
B [auth F]	PF13155	e6n9uF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PF13155	ECOD (1.6)
C [auth H]	PF00476	e6n9uH4	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: PF00476	ECOD (1.6)
C [auth H]	PF00476	e6n9uH2	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: PF00476	ECOD (1.6)
C [auth H]	PF00476	e6n9uH3	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: PF00476	ECOD (1.6)
C [auth H]	PF13482	e6n9uH1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF13482	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], B [auth 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 [auth E], B [auth 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 [auth E], B [auth F]	DNA primase/helicase	ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase 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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 DNA-directed 5'-3' RNA polymerase activity DNA primase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups 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	cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process viral genome replication cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process viral genome replication organic cyclic compound biosynthetic process organic substance biosynthetic process viral process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process	-
C [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 organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 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 organic cyclic compound 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	cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process viral genome replication cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process viral genome replication organic cyclic compound biosynthetic process organic substance biosynthetic process viral process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA synthesis involved in DNA replication DNA replication DNA-templated DNA replication	-
D [auth P]	RNA (5'-R(APCPCPAPG)-D(P(DOC))-3')	-	-	-
E [auth T]	DNA (44-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], B [auth F]	IPR048774	Bacteriophage T7 DNA helicase/primase, N-terminal	Domain
A [auth E], B [auth F]	IPR013237	Bacteriophage T7, Gp4, DNA primase/helicase, N-terminal	Domain
A [auth E], B [auth F]	IPR007694	DNA helicase, DnaB-like, C-terminal	Domain
A [auth E], B [auth F]	IPR006171	TOPRIM domain	Domain
A [auth E], B [auth F]	IPR034154	Archaeal primase DnaG/twinkle-like, TOPRIM domain	Domain
A [auth E], B [auth F]	IPR046394	Bacteriophage T7 DNA helicase/primase	Family
A [auth E], B [auth F]	IPR027032	Twinkle-like protein	Family
A [auth E], B [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth H]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth H]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth H]	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
C [auth H]	IPR034699	DNA-directed DNA polymerase T7	Family
C [auth H]	IPR002298	DNA polymerase A	Family
C [auth H]	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
C [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 R01GM133198.