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241  structures 5243  species 16  interactions 18116  sequences 64  architectures

Clan: DNA_clamp (CL0060)

Summary

DNA clamp superfamily Add an annotation

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 10 families and the total number of domains in the clan is 18116. The clan was built by A Bateman.

Literature references

  1. Neuwald AF; , Nucleic Acids Res 2003;31:4503-4516.: Evolutionary clues to DNA polymerase III beta clamp structural mechanisms. PUBMED:12888511 EPMC:12888511
  2. 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 10 member families:

DNA_pol3_beta DNA_pol3_beta_2 DNA_pol3_beta_3 DNA_PPF Herpes_UL42 Hus1 PCNA_C PCNA_N Rad1 Rad9

External database links

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) 4914 (27.1%) View
DNA_pol3_beta_3 (PF02768) 4819 (26.6%) View
DNA_pol3_beta (PF00712) 4817 (26.6%) View
PCNA_N (PF00705) 917 (5.1%) View
PCNA_C (PF02747) 906 (5.0%) View
DNA_PPF (PF02916) 530 (2.9%) View
Rad9 (PF04139) 382 (2.1%) View
Rad1 (PF02144) 354 (2.0%) View
Hus1 (PF04005) 342 (1.9%) View
Herpes_UL42 (PF02282) 135 (0.7%) View
Total: 10 Total: 18116 Clan alignment
 

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Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Interactions

There are 16 interactions for this clan. More...

Interacting families
A B
Herpes_UL42 Herpes_UL42
DNAPolymera_Pol
DNA_pol3_beta DNA_pol3_beta_2
DNA_pol3_beta_3
DNA_pol3_beta_2 DNA_pol3_beta
DNA_pol3_beta_3
DNA_pol3_delta
DNA_pol3_beta_3 DNA_pol3_beta
DNA_pol3_beta_2
DNA_pol3_delta
DNA_PPF gp45-slide_C
PCNA_C PCNA_N
XPG_I
PCNA_C
PCNA_N PCNA_N
PCNA_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 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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