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26  structures 359  species 1  interaction 530  sequences 9  architectures

Family: DNA_PPF (PF02916)

Summary: DNA polymerase processivity factor

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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.

DNA polymerase processivity factor Provide feedback

No Pfam abstract.

Literature references

  1. Shamoo Y, Steitz TA; , Cell. 1999;99:155-166.: Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. PUBMED:10535734 EPMC:10535734


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004190

The DNA polymerase processivity factor is a replisome sliding clamp subunit, which is responsible for tethering the catalytic subunit of DNA polymerase to the DNA during high speed replication. The crystal structure of the Bacteriophage RB69 sliding clamp has been solved. It has shown that the peptide binds to the sliding clamp at the same position as that of a replication inhibitor peptide bound to PCNA. This suggests that the replication inhibitor protein p21CIP1 competes with eukaryotic polymerases for the same binding pocket on the clamp [PUBMED:10535734].

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 10 members:

DNA_pol3_beta DNA_pol3_beta_2 DNA_pol3_beta_3 DNA_PPF 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(11)
Full
(530)
Representative proteomes NCBI
(382)
Meta
(453)
RP15
(2)
RP35
(4)
RP55
(14)
RP75
(20)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(11)
Full
(530)
Representative proteomes NCBI
(382)
Meta
(453)
RP15
(2)
RP35
(4)
RP55
(14)
RP75
(20)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(11)
Full
(530)
Representative proteomes NCBI
(382)
Meta
(453)
RP15
(2)
RP35
(4)
RP55
(14)
RP75
(20)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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: Structural domain
Previous IDs: none
Type: Domain
Author: Griffiths-Jones SR
Number in seed: 11
Number in full: 530
Average length of the domain: 114.60 aa
Average identity of full alignment: 54 %
Average coverage of the sequence by the domain: 23.78 %

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 25.0 25.0
Trusted cut-off 25.1 26.1
Noise cut-off 24.7 24.5
Model length: 110
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There is 1 interaction for this family. More...

gp45-slide_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_PPF domain has been found. There are 26 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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