6BBM

Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex

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)
C	SCOP2B Superfamily	N-terminal domain of DnaB helicase	8038007	3000700	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	N-terminal domain of DnaB helicase	8038007	3000700	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	N-terminal domain of DnaB helicase	8038007	3000700	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	N-terminal domain of DnaB helicase	8038007	3000700	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	N-terminal domain of DnaB helicase	8038007	3000700	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	N-terminal domain of DnaB helicase	8038007	3000700	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)
C	DnaB_1st	e6bbmC1	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: DnaB_1st	ECOD (1.6)
C	DnaB_C	e6bbmC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DnaB_C	ECOD (1.6)
D	DnaB_1st	e6bbmD1	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: DnaB_1st	ECOD (1.6)
D	DnaB_C	e6bbmD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DnaB_C	ECOD (1.6)
E	DnaB_1st	e6bbmE1	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: DnaB_1st	ECOD (1.6)
E	DnaB_C	e6bbmE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DnaB_C	ECOD (1.6)
F	DnaB_1st	e6bbmF1	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: DnaB_1st	ECOD (1.6)
F	DnaB_C	e6bbmF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DnaB_C	ECOD (1.6)
A	DnaB_1st	e6bbmA1	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: DnaB_1st	ECOD (1.6)
A	DnaB_C	e6bbmA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DnaB_C	ECOD (1.6)
B	DnaB_1st	e6bbmB2	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: DnaB_1st	ECOD (1.6)
B	DnaB_C	e6bbmB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DnaB_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	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, C, D, E A, B, C, D, E, F	Replicative DNA 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 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 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 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 DNA binding nucleic acid binding single-stranded 3'-5' DNA helicase activity single-stranded DNA helicase activity 3'-5' DNA helicase activity four-way junction helicase activity isomerase 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 identical protein binding protein binding double-stranded DNA helicase activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation DNA-templated DNA replication maintenance of fidelity replication fork processing DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation DNA-templated DNA replication maintenance of fidelity replication fork processing DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus	primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex pre-primosome complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome DnaB-DnaC-Rep-PriC complex primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex pre-primosome complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome DnaB-DnaC-Rep-PriC complex DnaB-DnaC-DnaT-PriA-PriC complex cytoplasm cytosol DnaB-DnaC complex catalytic complex core primosome complex DnaB-DnaG complex DNA helicase complex DnaB-DnaC-DnaT-PriA-PriB complex
G [auth V], H [auth W], I [auth X], J [auth Y], K [auth Z]	Replication protein P	-	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication 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	IPR007692	DNA helicase, DnaB type	Family
A, B, C, D, E A, B, C, D, E, F	IPR003593	AAA+ ATPase domain	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	IPR016136	DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR007693	DNA helicase, DnaB-like, 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	IPR036185	DNA helicase, DnaB-like, N-terminal domain superfamily	Homologous Superfamily
G [auth V], H [auth W], I [auth X], J [auth Y], K [auth Z]	IPR009731	Replication P-like	Family

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.