4ESV | pdb_00004esv

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth A]DnaB_1ste4esvA4 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
C [auth A]DnaB_Ce4esvA3 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
H [auth F]DnaB_1ste4esvF2 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
H [auth F]DnaB_Ce4esvF1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
K [auth I]DnaB_1ste4esvI2 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
K [auth I]DnaB_Ce4esvI1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
L [auth J]DnaB_1ste4esvJ3 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
L [auth J]DnaB_Ce4esvJ2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
N [auth L]DnaB_1ste4esvL3 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
N [auth L]DnaB_Ce4esvL2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
M [auth K]DnaB_1ste4esvK2 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
M [auth K]DnaB_Ce4esvK1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
J [auth H]DnaB_1ste4esvH2 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
J [auth H]DnaB_Ce4esvH1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
I [auth G]DnaB_1ste4esvG2 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
I [auth G]DnaB_Ce4esvG1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
G [auth E]DnaB_1ste4esvE3 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
G [auth E]DnaB_Ce4esvE2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
F [auth D]DnaB_1ste4esvD2 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
F [auth D]DnaB_Ce4esvD1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
E [auth C]DnaB_1ste4esvC1 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
E [auth C]DnaB_Ce4esvC2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)
D [auth B]DnaB_1ste4esvB4 A: alpha arraysX: DnaB helicase N-terminal domain-related (From Topology)H: DnaB helicase N-terminal domain-related (From Topology)T: DnaB helicase N-terminal domain-relatedF: DnaB_1stECOD (1.6)
D [auth B]DnaB_Ce4esvB3 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DnaB_CECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
C [auth A]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
C [auth A]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
H [auth F]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
H [auth F]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
K [auth I]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
K [auth I]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
L [auth J]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
L [auth J]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
N [auth L]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
N [auth L]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
M [auth K]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
M [auth K]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
J [auth H]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
J [auth H]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
I [auth G]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
I [auth G]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
G [auth E]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
G [auth E]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
F [auth D]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
F [auth D]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
E [auth C]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
E [auth C]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
D [auth B]1.10.860.10 Mainly Alpha Orthogonal Bundle DNAb Helicase Chain ACATH (4.3.0)
D [auth B]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03796DnaB-like helicase C terminal domain (DnaB_C)DnaB-like helicase C terminal domainThe 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
PF00772DnaB-like helicase N terminal domain (DnaB)DnaB-like helicase N terminal domainThe 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Replicative helicase
B [auth W]5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'---
A [auth V]5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR016136DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminalHomologous Superfamily
IPR007693DNA helicase, DnaB-like, N-terminalDomain
IPR007694DNA helicase, DnaB-like, C-terminalDomain
IPR007692DNA helicase, DnaB typeFamily
IPR036185DNA helicase, DnaB-like, N-terminal domain superfamilyHomologous Superfamily
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily