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183  structures 7866  species 7  interactions 8503  sequences 16  architectures

Family: DNA_pol3_beta_3 (PF02768)

Summary: DNA polymerase III beta subunit, C-terminal domain

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This is the Wikipedia entry entitled "DNA clamp". More...

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DNA polymerase III beta subunit, C-terminal domain Provide feedback

A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.

Literature references

  1. Kong XP, Onrust R, O'Donnell M, Kuriyan J; , Cell 1992;69:425-437.: Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. PUBMED:1349852 EPMC:1349852


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022635

DNA polymerase III is a complex, multichain holoenzyme responsible for most of the replicative synthesis in bacteria [PUBMED:8548826]. It functions by adding nucleotide triphosphate (dNTP) residues to the 5'-end of a growing DNA chain, using a complementary DNA as template. The elongation factor beta-clamp, also called beta subunit, is part of the DNA polymerase III holoenzyme. However, beta-clamp is not attached to polymerase III permanently like the other subunits. It is loaded on the DNA, by clamp loader, a subunit of DNA Pol III [PUBMED:27499105].

The beta clamp forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The bacterial beta clamp is a homodimer; each monomer consists of three globular domains to yield a six-domain ring [PUBMED:18191219]. It is structurally similar to the trimeric ring formed by proliferating cell nuclear antigen (PCNA) (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69) [PUBMED:1358275]. This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.

This entry describes the C-terminal domain of the beta sliding clamp.

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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Pfam Clan

This family is a member of clan DNA_clamp (CL0060), which has the following description:

Sliding DNA clamps are ring-shaped proteins that allow DNA polymerase to achieve high processivity during chromosome replication by tethering the polymerase catalytic subunit to DNA. All of the structures share a 12-fold symmetry around the ring consisting of a simple structural repeat, though there is structural divergence in some of the repeats. Bacterial beta-clamps contain six repeats per subunit with two subunits per ring while the eukaryotic and bacteriophage clamps contain four repeats per subunit with three subunits per ring. Pairs of these repeats form a domain, which has been termed the 'processivity fold'; thus the ring of the sliding clamp contains six domains and therefore is often described as having 6-fold symmetry. A structural representative of a fourth family of processivity fold proteins, namely the herpes simplex virus UL42 protein, is also available. UL42 does not form a ring-shaped clamp, however, but rather functions as a monomer and interacts with DNA quite differently than do sliding clamps; it has been suggested that UL42 resembles a primitive ancestor of sliding clamps [2].

The clan contains the following 13 members:

DNA_pol3_beta DNA_pol3_beta_2 DNA_pol3_beta_3 DNA_PPF gp45-slide_C Herpes_DNAp_acc Herpes_PAP Herpes_UL42 Hus1 PCNA_C PCNA_N Rad1 Rad9

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(12)
Full
(8503)
Representative proteomes UniProt
(24560)
NCBI
(26271)
Meta
(2447)
RP15
(2415)
RP35
(6053)
RP55
(8861)
RP75
(12479)
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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
(12)
Full
(8503)
Representative proteomes UniProt
(24560)
NCBI
(26271)
Meta
(2447)
RP15
(2415)
RP35
(6053)
RP55
(8861)
RP75
(12479)
Alignment:
Format:
Order:
Sequence:
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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
(12)
Full
(8503)
Representative proteomes UniProt
(24560)
NCBI
(26271)
Meta
(2447)
RP15
(2415)
RP35
(6053)
RP55
(8861)
RP75
(12479)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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_631 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR
Number in seed: 12
Number in full: 8503
Average length of the domain: 121.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 32.75 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 121
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Interactions

There are 7 interactions for this family. More...

DNA_pol3_delta DNA_pol3_beta_3 DNA_pol3_beta_2 DNA_pol3_beta DNA_pol3_beta DNA_pol3_beta_2 IMS_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 DNA_pol3_beta_3 domain has been found. There are 183 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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