InterPro domain: IPR022312

DNA carries the biological information that instructs cells how to existin an ordered fashion: accurate replication is thus one of the mostimportant events in the cell life cycle. This function is mediated byDNA-directed DNA-polymerases, which add nucleotide triphosphate (dNTP)residues to the 3'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers forchain elongation, although terminal proteins may also be used. Three motifs, A, B and C [ 1 ], 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 [ 2 ].

DNA polymerases ( 2.7.7.7 ) can be classified, on the basis of sequencesimilarity [ 2 , 3 ], into at least four different groups: A, B, C and X. Members of family X are small (about 40kDa) compared with other polymerases and encompass two distinct polymerase enzymes that have similar functionality: vertebrate polymerase beta (same as yeast pol 4), and terminal deoxynucleotidyl-transferase (TdT) ( 2.7.7.31 ). The former functions in DNA repair, whilethe latter terminally adds single nucleotides to polydeoxynucleotide chains.Both enzymes catalyse addition of nucleotides in a distributive manner, i.e. theydissociate from the template-primer after addition of each nucleotide.DNA-polymerases show a degree of structural similarity with RNA-polymerases.

Family X DNA polymerases (PolX) are involved in DNA repair, being evolutionarily conserved in prokaryotes, eukaryotes and archaea. All DNA polymerases from this family are single-subunit enzymes, lacking the 3'-5' exonuclease activity and displaying very low processivity during primer extension reactions [ 3 ]. Proteins in this family include in the well-characterized mammalian Pol beta; more recently discovered eukaryotic polymerases lambda, and mu; and a template-independent polymerase, terminal transferase (TdT) [ 4 ].

In eukaryotes, Pol beta fills short nucleotide gaps produced during base excision repair (BER) [ 5 ]. Pols beta, lamda, mu can also take part in translesion DNA synthesis (TLS) [ 5 ]. Their structures have been revealed [ 6 , 7 , 8 ].

1. An attempt to unify the structure of polymerases. Protein Eng. 3, 461-7
2. Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases. Proc. Natl. Acad. Sci. U.S.A. 84, 8287-91
3. Characterization of SpPol4, a unique X-family DNA polymerase in Schizosaccharomyces pombe. Nucleic Acids Res 33, 4762-74
4. Functions of DNA polymerases. Adv Protein Chem 69, 137-65
5. Eukaryotic DNA polymerases. Curr Opin Struct Biol 53, 77-87
6. Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Nat Commun 8, 253
7. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science 264, 1891-903
8. A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. EMBO J 35, 2045-59