3GXV

Three-dimensional structure of N-terminal domain of DnaB Helicase from Helicobacter pylori and its interactions with primase

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)
A	PF00772	e3gxvA1	A: alpha arrays	X: DnaB helicase N-terminal domain-related (From Topology)	H: DnaB helicase N-terminal domain-related (From Topology)	T: DnaB helicase N-terminal domain-related	F: PF00772	ECOD (1.6)
B	PF00772	e3gxvB1	A: alpha arrays	X: DnaB helicase N-terminal domain-related (From Topology)	H: DnaB helicase N-terminal domain-related (From Topology)	T: DnaB helicase N-terminal domain-related	F: PF00772	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.860.10	Mainly Alpha	Orthogonal Bundle	DNAb Helicase	Chain A	CATH (4.3.0)
B	1.10.860.10	Mainly Alpha	Orthogonal Bundle	DNAb Helicase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00772	DnaB-like helicase N terminal domain (DnaB)	DnaB-like helicase N 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 N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity [1].	Domain
C	PF00772	DnaB-like helicase N terminal domain (DnaB)	DnaB-like helicase N 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 N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity [1].	Domain
D	PF00772	DnaB-like helicase N terminal domain (DnaB)	DnaB-like helicase N 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 N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Replicative DNA helicase	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 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 catalytic activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity identical protein binding protein binding	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 cytoplasm cytosol
C	Replicative DNA helicase	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 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 catalytic activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity identical protein binding protein binding	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 cytoplasm cytosol
D	Replicative DNA helicase	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 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 catalytic activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity identical protein binding protein binding	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 cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016136	DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal	Homologous Superfamily
A, B	IPR007693	DNA helicase, DnaB-like, N-terminal	Domain
A, B	IPR007694	DNA helicase, DnaB-like, C-terminal	Domain
A, B	IPR007692	DNA helicase, DnaB type	Family
A, B	IPR036185	DNA helicase, DnaB-like, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR016136	DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal	Homologous Superfamily
C	IPR007693	DNA helicase, DnaB-like, N-terminal	Domain
C	IPR007694	DNA helicase, DnaB-like, C-terminal	Domain
C	IPR007692	DNA helicase, DnaB type	Family
C	IPR036185	DNA helicase, DnaB-like, N-terminal domain superfamily	Homologous Superfamily
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D	IPR016136	DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal	Homologous Superfamily
D	IPR007693	DNA helicase, DnaB-like, N-terminal	Domain
D	IPR007694	DNA helicase, DnaB-like, C-terminal	Domain
D	IPR007692	DNA helicase, DnaB type	Family
D	IPR036185	DNA helicase, DnaB-like, N-terminal domain superfamily	Homologous Superfamily
D	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.