4M4W | pdb_00004m4w

Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
O	Bac_DnaA_N	e4m4wO1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
O	DnaI_N	e4m4wO3	A: few secondary structure elements	X: N-terminal domain of helicase-loading protein DnaI (From Topology)	H: N-terminal domain of helicase-loading protein DnaI (From Topology)	T: N-terminal domain of helicase-loading protein DnaI	F: DnaI_N	ECOD (1.6)
N	Bac_DnaA_N	e4m4wN1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
N	DnaI_N	e4m4wN2	A: few secondary structure elements	X: N-terminal domain of helicase-loading protein DnaI (From Topology)	H: N-terminal domain of helicase-loading protein DnaI (From Topology)	T: N-terminal domain of helicase-loading protein DnaI	F: DnaI_N	ECOD (1.6)
M	Bac_DnaA_N	e4m4wM5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
M	DnaI_N	e4m4wM6	A: few secondary structure elements	X: N-terminal domain of helicase-loading protein DnaI (From Topology)	H: N-terminal domain of helicase-loading protein DnaI (From Topology)	T: N-terminal domain of helicase-loading protein DnaI	F: DnaI_N	ECOD (1.6)
L	Bac_DnaA_N	e4m4wL2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
L	DnaI_N	e4m4wL3	A: few secondary structure elements	X: N-terminal domain of helicase-loading protein DnaI (From Topology)	H: N-terminal domain of helicase-loading protein DnaI (From Topology)	T: N-terminal domain of helicase-loading protein DnaI	F: DnaI_N	ECOD (1.6)
K	Bac_DnaA_N	e4m4wK4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
K	DnaI_N	e4m4wK5	A: few secondary structure elements	X: N-terminal domain of helicase-loading protein DnaI (From Topology)	H: N-terminal domain of helicase-loading protein DnaI (From Topology)	T: N-terminal domain of helicase-loading protein DnaI	F: DnaI_N	ECOD (1.6)
J	Bac_DnaA_N	e4m4wJ2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
J	DnaI_N	e4m4wJ3	A: few secondary structure elements	X: N-terminal domain of helicase-loading protein DnaI (From Topology)	H: N-terminal domain of helicase-loading protein DnaI (From Topology)	T: N-terminal domain of helicase-loading protein DnaI	F: DnaI_N	ECOD (1.6)
I	DnaB_1st	e4m4wI1	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)
H	DnaB_1st	e4m4wH1	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)
G	DnaB_1st	e4m4wG1	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_1st	e4m4wF4	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	e4m4wF2	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	e4m4wE4	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	e4m4wE2	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	e4m4wD4	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	e4m4wD2	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)
C	DnaB_1st	e4m4wC4	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	e4m4wC2	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	e4m4wB4	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	e4m4wB2	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	e4m4wA4	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	e4m4wA2	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
J, K, L, M, N J, K, L, M, N, O	PF00308	Bacterial DnaA ATPAse domain (Bac_DnaA)	Bacterial DnaA ATPAse domain	This entry represents the ATPAse domain of DnaA and similar proteins.	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J, K, L, M, N J, K, L, M, N, O	Primosomal protein DnaI	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 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 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 cation binding metal ion binding	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, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic 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, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process	primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome cytoplasm
G, H, I	DNA primase	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 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 DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding metal ion binding ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA helicase activity macromolecular conformation isomerase activity ATP-dependent activity	DNA-templated DNA replication DNA replication, synthesis of primer 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 nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process DNA-templated DNA replication DNA replication, synthesis of primer 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 nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process cellular process macromolecule metabolic process	primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome cytoplasm transferase complex, transferring phosphorus-containing groups primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome cytoplasm transferase complex, transferring phosphorus-containing groups catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
A, B, C, D, E A, B, C, D, E, F	Replicative helicase	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 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 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 nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity identical protein binding protein binding	DNA-templated DNA replication DNA replication, synthesis of primer 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 nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process DNA-templated DNA replication DNA replication, synthesis of primer 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 nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process cellular process macromolecule metabolic process	primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J, K, L, M, N J, K, L, M, N, O	IPR003593	AAA+ ATPase domain	Domain
J, K, L, M, N J, K, L, M, N, O	IPR009928	Primosomal DnaI, N-terminal	Domain
J, K, L, M, N J, K, L, M, N, O	IPR013317	Chromosomal replication initiator protein DnaA, ATPAse domain	Domain
J, K, L, M, N J, K, L, M, N, O	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
G, H, I	IPR037068	DNA primase, catalytic core, N-terminal domain superfamily	Homologous Superfamily
G, H, I	IPR016136	DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal	Homologous Superfamily
G, H, I	IPR034151	Bacterial DnaG primase, TOPRIM domain	Domain
G, H, I	IPR030846	DNA primase DnaG, bacteria	Family
G, H, I	IPR006295	DNA primase, DnaG	Domain
G, H, I	IPR006171	TOPRIM domain	Domain
G, H, I	IPR002694	Zinc finger, CHC2-type	Domain
G, H, I	IPR036977	DNA Primase, CHC2-type zinc finger	Homologous Superfamily
G, H, I	IPR013264	DNA primase DNAG, catalytic core, N-terminal	Domain
G, H, I	IPR036185	DNA helicase, DnaB-like, N-terminal domain superfamily	Homologous Superfamily
G, H, I	IPR050219	DnaG Primase	Family
G, H, I	IPR019475	DNA primase, DnaB-helicase binding domain	Domain
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	IPR007692	DNA helicase, DnaB type	Family
A, B, C, D, E A, B, C, D, E, F	IPR036185	DNA helicase, DnaB-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily