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45  structures 4498  species 2  interactions 5852  sequences 42  architectures

Family: DnaB (PF00772)

Summary: DnaB-like helicase N terminal domain

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This is the Wikipedia entry entitled "DnaB helicase". More...

DnaB helicase Edit Wikipedia article

Replicative DNA helicase
Identifiers
Symbol dnaB
Entrez 948555
UniProt P0ACB0
Other data
DnaB-like helicase N terminal domain
PDB 1jwe EBI.jpg
nmr structure of the n-terminal domain of e. coli dnab helicase
Identifiers
Symbol DnaB
Pfam PF00772
InterPro IPR007693
SCOP 1jwe
SUPERFAMILY 1jwe
DnaB-like helicase C terminal domain
Identifiers
Symbol DnaB_C
Pfam PF03796
Pfam clan CL0023
InterPro IPR007694

DnaB helicase is an enzyme in bacteria which opens the replication fork during DNA replication. 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.[1] Initially when DnaB binds to dnaA, it is associated with dnaC, a negative regulator. After DnaC dissociates, DnaB binds dnaG.

The N-terminal has a multi-helical structure that forms an orthogonal bundle.[1] The C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

In eukaryotes, helicase function is provided by the MCM (Minichromosome maintenance) complex.

The DnaB helicase is the product of the dnaB gene. The helicase enzyme that is produced is a hexamer in E. coli, as well as in many other bacteria. The energy for DnaB activity is provided by NTP hydrolysis. Mechanical energy moves the DnaB into the replication fork, physically splitting it in half.

E. coli dnaB[edit]

In E. coli, dnaB is a hexameric protein of six 471-residue subunits, which form a ring-shaped structure with threefold symmetry. During DNA replication, the lagging strand of DNA binds in the central channel of dnaB, and the second DNA strand is excluded. The binding of dNTPs causes a conformational change which allows the dnaB to translocate along the DNA, thus mechanically forcing the separation of the DNA strands.

Mechanism of initiation of replication[edit]

At least 10 different enzymes or proteins participate in the initiation phase of replication. They open the DNA helix at the origin and establish a prepriming complex for subsequent reactions. The crucial component in the initiation process is the DnaA protein, a member of the AAA+ ATPase protein family (ATPases associated with diverse cellular activities). Many AAA+ ATPases, including DnaA, form oligomers and hydrolyze ATP relatively slowly. This ATP hydrolysis acts as a switch mediating interconversion of the protein between two states. In the case of DnaA, the ATP-bound form is active and the ADP-bound form is inactive.

Eight DnaA protein molecules, all in the ATP-bound state, assemble to form a helical complex encompassing the R and I sites in oriC. DnaA has a higher affinity for the R sites than I sites, and binds R sites equally well in its ATP or ADP-bound form. The I sites, which bind only the ATP-bound DnaA, allow discrimination between the active and inactive forms of DnaA. The tight right-handed wrapping of the DNA around this complex introduces an effective positive supercoil. The associated strain in the nearby DNA leads to denaturation in the A:T-rich 'DUE' (DNA Unwinding Element)region. The complex formed at the replication origin also includes several DNA-binding proteins- Hu, IHF and FIS that facilitate DNA bending.

The DnaC protein, another AAA+ ATPase, then loads the DnaB protein onto the separated DNA strands in the denatured region. A hexamer of DnaC, each subunit bound to ATP, forms a tight complex with the hexameric, ring-shaped DnaB helicase. This DnaC-DnaB interaction opens the DnaB ring, the process being aided by a further interaction between DnaB and DnaA. Two of the ring-shaped DnaB hexamers are loaded in the DUE, one onto each DNA strand. The ATP bound to DnaC is hydrolyzed, releasing the DnaC and leaving the DnaB bound to the DNA.

Loading of the DnaB helicase is the key step in replication initiation. As a replicative helicase, DnaB migrates along the single-stranded DNA in the 5'→3' direction, unwinding the DNA as it travels. The DnaB helicases loaded onto the two DNA strands thus travel in opposite directions, creating two potential replication forks. All other proteins at the replication fork are linked directly or indirectly to DnaB.

External links[edit]

References[edit]

  1. ^ a b Fass D, Bogden CE, Berger JM (June 1999). "Crystal structure of the N-terminal domain of the DnaB hexameric helicase". Structure 7 (6): 691–8. PMID 10404598. 

This article incorporates text from the public domain Pfam and InterPro IPR007693

This article incorporates text from the public domain Pfam and InterPro IPR007694

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

DnaB-like helicase N terminal domain Provide feedback

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].

Literature references

  1. Fass D, Bogden CE, Berger JM; , Structure Fold Des 1999;7:691-698.: Crystal structure of the N-terminal domain of the DnaB hexameric helicase. PUBMED:10404598 EPMC:10404598


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007693

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 dimerization 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. This domain has a multi-helical structure that forms an orthogonal bundle [PUBMED:10404598].

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(156)
Full
(5852)
Representative proteomes NCBI
(3975)
Meta
(2460)
RP15
(376)
RP35
(752)
RP55
(973)
RP75
(1143)
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  Seed
(156)
Full
(5852)
Representative proteomes NCBI
(3975)
Meta
(2460)
RP15
(376)
RP35
(752)
RP55
(973)
RP75
(1143)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Pfam alignments:

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Curation and family details

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Seed source: Pfam-B_1000 (release 2.1)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 156
Number in full: 5852
Average length of the domain: 101.40 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 21.41 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 103
Family (HMM) version: 16
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Species distribution

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Interactions

There are 2 interactions for this family. More...

DnaB DnaB_C

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DnaB domain has been found. There are 45 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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