Domain

DNA-directed DNA polymerase X (IPR002054)

Short name: DNA-dir_DNA_pol_X

Domain relationships

None.

Description

DNA carries the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA-polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. Three motifs, A, B and C [PMID: 2196557], are seen to be conserved across all DNA-polymerases, with motifs A and C also seen in RNA- polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (Escherichia coli) structure: motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure [PMID: 2196557].

DNA polymerases (EC:2.7.7.7) can be classified, on the basis of sequence similarity [PMID: 3479792, PMID: 2196557], into at least four different groups: A, B, C and X. X family polymerases fill in short gaps during DNA repair, and are small (about 40 kDa) compared with other polymerases. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination [PMID: 16061182, PMID: 15100289]. X family polymerases include eukaryotic Pol beta, Pol lambda, Pol mu and terminal deoxynucleotidyl-transferase (TdT) (EC:2.7.7.31). Pol beta and Pol lambda are primarily DNA template-dependent polymerases, whereas TdT is a DNA template-independent polymerase [PMID: 18972388]. Pol mu has both template dependent and template independent activities [PMID: 17159995]. These enzymes catalyse addition of nucleotides in a distributive manner, i.e. they dissociate from the template-primer after addition of each nucleotide. DNA-polymerases show a degree of structural similarity with RNA-polymerases.

This domain is found either at the extreme N or C termini of DNA polymerase X proteins.

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
CDD
SMART