Summary
DNA clamp superfamily
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].
This clan contains 13 families and the total number of domains in the clan is 37344. The clan was built by A Bateman.
Literature references
- Neuwald AF; , Nucleic Acids Res 2003;31:4503-4516.: Evolutionary clues to DNA polymerase III beta clamp structural mechanisms. PUBMED:12888511 EPMC:12888511
- Neuwald AF, Poleksic A; , Nucleic Acids Res 2000;28:3570-3580.: PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. PUBMED:10982878 EPMC:10982878
Members
This clan contains the following 13 member families:
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 Rad9External database links
| CATH: | 3.70.10.20 |
| SCOP: | 55979 |
Domain organisation
Below is a listing of the unique domain organisations or architectures from this clan. More...
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Alignments
The table below shows the number of occurrences of each domain throughout the sequence database. More...
| Pfam family | Num. domains | Alignment |
|---|---|---|
| DNA_pol3_beta_2 (PF02767) | 8917 (23.9%) | View |
| DNA_pol3_beta (PF00712) | 8607 (23.0%) | View |
| DNA_pol3_beta_3 (PF02768) | 8571 (23.0%) | View |
| PCNA_C (PF02747) | 2638 (7.1%) | View |
| PCNA_N (PF00705) | 2532 (6.8%) | View |
| Rad9 (PF04139) | 2093 (5.6%) | View |
| Rad1 (PF02144) | 1799 (4.8%) | View |
| Hus1 (PF04005) | 1794 (4.8%) | View |
| gp45-slide_C (PF09116) | 165 (0.4%) | View |
| DNA_PPF (PF02916) | 128 (0.3%) | View |
| Herpes_UL42 (PF02282) | 49 (0.1%) | View |
| Herpes_DNAp_acc (PF04929) | 26 (0.1%) | View |
| Herpes_PAP (PF03325) | 25 (0.1%) | View |
| Total: 13 | Total: 37344 | Clan alignment |
Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.
Family relationships
This diagram shows the relationships between members of this clan. More...
Species distribution
Tree controls
HideThis tree shows the occurrence of the domains in this clan across different species. 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 MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.
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