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94  structures 7214  species 0  interactions 9931  sequences 50  architectures

Family: DnaB (PF00772)

Summary: DnaB-like helicase N terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

DnaB helicase Edit Wikipedia article

dnaB helicase is an enzyme which holds open the replication fork during DNA replication.

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


Internal database links

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

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(154)
Full
(9931)
Representative proteomes UniProt
(52946)
RP15
(1545)
RP35
(5075)
RP55
(10377)
RP75
(17999)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(154)
Full
(9931)
Representative proteomes UniProt
(52946)
RP15
(1545)
RP35
(5075)
RP55
(10377)
RP75
(17999)
Alignment:
Format:
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Sequence:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(154)
Full
(9931)
Representative proteomes UniProt
(52946)
RP15
(1545)
RP35
(5075)
RP55
(10377)
RP75
(17999)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1000 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 154
Number in full: 9931
Average length of the domain: 102 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 20.9 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 103
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 94 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077ZI46 View 3D Structure Click here
A0A0H3GP89 View 3D Structure Click here
A0A0H3GQ64 View 3D Structure Click here
A0A0H3GVK5 View 3D Structure Click here
K0F8Z6 View 3D Structure Click here
O25916 View 3D Structure Click here
O83097 View 3D Structure Click here
P0A1Q4 View 3D Structure Click here
P0ACB0 View 3D Structure Click here
P0ACB1 View 3D Structure Click here
P37469 View 3D Structure Click here
P45256 View 3D Structure Click here
P46394 View 3D Structure Click here
P57611 View 3D Structure Click here
P9WMR3 View 3D Structure Click here
Q0PAV4 View 3D Structure Click here
Q1RI04 View 3D Structure Click here
Q2FY11 View 3D Structure Click here
Q2G1S4 View 3D Structure Click here
Q327V9 View 3D Structure Click here
Q55418 View 3D Structure Click here
Q5F7R0 View 3D Structure Click here
Q5F9B4 View 3D Structure Click here
Q5F9E7 View 3D Structure Click here
Q5HNY6 View 3D Structure Click here
Q6ABX1 View 3D Structure Click here
Q89A52 View 3D Structure Click here
Q8DMZ2 View 3D Structure Click here
Q8X5V3 View 3D Structure Click here
Q8YZA1 View 3D Structure Click here
Q9CNL6 View 3D Structure Click here
Q9HUN3 View 3D Structure Click here
Q9ZD08 View 3D Structure Click here
X8FMD5 View 3D Structure Click here
X8FMS3 View 3D Structure Click here