Structure and function relationships in mammalian DNA polymerases

Abstract

DNA polymerases are vital for the synthesis of new DNA strands. Since the discovery of DNA polymerase I in Escherichia coli, a diverse library of mammalian DNA polymerases involved in DNA replication, DNA repair, antibody generation, and cell checkpoint signaling has emerged. While the unique functions of these DNA polymerases are differentiated by their association with accessory factors and/or the presence of distinctive catalytic domains, atomic resolution structures of DNA polymerases in complex with their DNA substrates have revealed mechanistic subtleties that contribute to their specialization. In this review, the structure and function of all 15 mammalian DNA polymerases from families B, Y, X, and A will be reviewed and discussed with special emphasis on the insights gleaned from recently published atomic resolution structures.

Keywords: DNA polymerase; DNA repair; DNA synthesis; Replication; Structural biology.

Fig. 1

Overall structure and specific features of replicative B-family polymerases. a Surface representations of human pol α (5IUD), yeast pol δ (3IAY) and yeast pol ɛ (4M8O) are shown with their exonuclease (orange), P-domain (yellow), fingers (cyan), thumb (green), palm (blue), and N-terminal (red) domains highlighted. b A close-up view of the pol α thumb domain (green) making contact with the 2′-OH groups of the RNA of its DNA/RNA hybrid substrate (white sticks), the product of its primase activity (4Q5V). c The minor groove of nascent DNA probed by Pol δ through direct contacts (blue sticks), as well as through coordinated water-bridges (cyan spheres; 3IAY). d The P-domain (yellow), found only in Pol ɛ, provides additional contact to the nascent DNA (gray surface; 4M8O)

Fig. 2

Y-family polymerases. Unique lesion bypass mechanisms of a templating lesion and incoming nucleotide are indicated (white sticks). a human Pol η shown in surface (green; 3MR3) b human Pol ι shown in cartoon (green; 2DPJ) c human Pol κ shown in surface with indicated catalytic core (green), PAD (yellow), and N-clasp (cyan) (4U7C) d yeast Rev1 shown in cartoon with undamaged templating guanine (green; 2AQ4), overlayed with damaged guanine template (white) and residues (cyan sticks; 5WM1)

Fig. 3

The different structural features of the polymerase X-family members and their substrates. a A representative pre-catalytic structure of each X-family member highlighting the similarities and differences between the DNA substrate (orange), the incoming dNTP (yellow sticks), and the structural domains: Catalytic (gray), BRCT (magenta), 8 kD (blue), and Loop 1 (green) (left to right) 2FMS, 2PFP, 5TXX, 4I27 b Structural comparison of Pol μ (gray), Loop 1 (green) and DNA (orange) between the apoprotein (4LZD) and DNA-bound (5TXX) structures. c Structural comparison of Loop 1 (green) in TdT (gray) with different DNA (orange) substrates (left to right) 4I27, 4QZ8 and 5D46

Fig. 4

A-Family polymerases. a Domain and subdomain structure of pol γ (3IKM). b Ternary structure of pol θ (green) bypassing an AP site, highlighting the DNA contacts at the primer terminus (4X0P). c Overlay of pol ν open (yellow; 4XVL) and closed (green; 4XVK) binary complexes