Nucleotidyltransferase (NT) domain of family X DNA Polymerases.
X family polymerases fill in short gaps during DNA repair. 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. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
Comment:The active site annotation includes NTP- and primer-binding residues, and the binding site for two magnesium ions (the nucleotide binding ion, and the catalytic ion).
Structure:2BPF_A, Rat DNA Pol beta bound with a primer, ddCTP, and 2 magnesium ions; contacts determined at 4A.
Jiyao W et al.(2023). "The conserved domain database in 2023.",