Molecular Life Sciences

Living Edition
| Editors: Robert D. Wells, Judith S. Bond, Judith Klinman, Bettie Sue Siler Masters, Ellis Bell

DNA Polymerase III Structure

  • Charles McHenry
Living reference work entry


By itself, the polymerase catalytic subunit of the DNA polymerase III holoenzyme (Pol III HE), α, exhibits no special properties that hint of the Pol III HE’s high catalytic efficiency, accuracy, and enormous processivity. These properties are gained by association with other proteins through a series of distinct protein interaction domains. A PHP domain at the N-terminus of Pol III α binds the proofreading subunit, ε. A typical Mg++-dependent polymerase catalytic domain has a fold similar to the DNA polymerase β (Pol X family). Adjacent to the polymerase domain is the β-binding domain. Interaction of this domain with the β2 sliding clamp processivity factor, together with an ε−β2interaction, provides the primary determinants of the enzyme’s processivity. The C-terminus contains two domains, one an OB fold that may bind single-stranded DNA and a τ-binding domain that binds the τ-subunit of the DnaX complex. X-ray crystal structures of Pol III α in the apoenzyme form, bound...


Polymerase Domain Exonuclease Domain Catalytic Aspartate Thumb Domain Palm Domain 
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  1. Aravind L, Koonin EV (1998) Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res 26:3746–3752PubMedCentralCrossRefPubMedGoogle Scholar
  2. Bailey S, Wing RA, Steitz TA (2006) The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell 126:893–904CrossRefPubMedGoogle Scholar
  3. Banos B, Lazaro JM, Villar L, Salas M, De Vega M (2008) Editing of misaligned 3′-termini by an intrinsic 3′-5′ exonuclease activity residing in the PHP domain of a family X DNA polymerase. Nucleic Acids Res 36:5736–5749PubMedCentralCrossRefPubMedGoogle Scholar
  4. Barnes MH, Leo CJ, Brown NC (1998) DNA polymerase III of Gram-positive eubacteria is a zinc metalloprotein conserving an essential finger-like domain. Biochemistry 37:15254–15260CrossRefPubMedGoogle Scholar
  5. Barros T, Guenther J, Kelch B, Anaya J, Prabhakar A, O’Donnell M, Kuriyan J, Lamers MH (2013) A structural role for the PHP domain in E. coli DNA polymerase III. BMC Struct Biol 13:8PubMedCentralCrossRefPubMedGoogle Scholar
  6. Blasius M, Shevelev I, Jolivet E, Sommer S, Hübscher U (2006) DNA polymerase X from Deinococcus radiodurans possesses a structure-modulated 3′ → 5′ exonuclease activity involved in radioresistance. Mol Microbiol 60:165–176CrossRefPubMedGoogle Scholar
  7. Bierne H, Vilette D, Ehrlich SD, Michel B (1997) Isolation of a dnaE mutation which enhances recA independent homologous recombination in the Escherichia coli chromosome. Mol Microbiol 24:1225–1234CrossRefPubMedGoogle Scholar
  8. Dalrymple BP, Kongsuwan K, Wijffels G, Dixon NE, Jennings PA (2001) A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc Natl Acad Sci U S A 98:11627–11632PubMedCentralCrossRefPubMedGoogle Scholar
  9. Doherty AJ, Serpell LC, Ponting CP (1996) The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res 24:2488–2497PubMedCentralCrossRefPubMedGoogle Scholar
  10. Dohrmann PR, McHenry CS (2005) A bipartite polymerase-processivity factor interaction: only the internal β binding site of the α subunit is required for processive replication by the DNA polymerase III holoenzyme. J Mol Biol 350:228–239CrossRefPubMedGoogle Scholar
  11. Dohrmann PR, Manhart CM, Downey CD, McHenry CS (2011) The rate of polymerase release upon filing the gap between Okazaki fragments is inadequate to support cycling during lagging strand synthesis. J Mol Biol 414:15–27PubMedCentralCrossRefPubMedGoogle Scholar
  12. Evans TC Jr, Martin D, Kolly R, Panne D, Sun L, Ghosh I, Chen L, Benner J, Liu XQ, Xu MQ (2000) Protein trans-splicing and cyclization by a naturally split intein from the dnaE gene of Synechocystis species PCC6803. J Biol Chem 275:9091–9094CrossRefPubMedGoogle Scholar
  13. Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC (2008) Structure of polC reveals unique DNA binding and fidelity determinants. Proc Natl Acad Sci U S A 105:20695–20700PubMedCentralCrossRefPubMedGoogle Scholar
  14. Fijalkowska IJ, Schaaper RM (1993) Antimutator mutations in the α subunit of Escherichia coli DNA polymerase III identification of the responsible mutations and alignment with other DNA polymerases. Genetics 134:1039–1044PubMedCentralPubMedGoogle Scholar
  15. Gulbis JM, Kazmirski SL, Finkelstein J, Kelman Z, O’Donnell ME, Kuriyan J (2004) Crystal structure of the chi:psi subassembly of the Escherichia coli DNA polymerase clamp-loader complex. Eur J Biochem 271:439–449CrossRefPubMedGoogle Scholar
  16. Hiratsuka K, Reha-Krantz LJ (2000) Identification of Escherichia coli dnaE (polC) mutants with altered sensitivity to 2′,3′-dideoxyadenosine. J Bacteriol 182:3942–3947PubMedCentralCrossRefPubMedGoogle Scholar
  17. Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE (2007) The unstructured C-terminus of the τ subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the α subunit. Nucleic Acids Res 35:2813–2824PubMedCentralCrossRefPubMedGoogle Scholar
  18. Jergic S, Horan NP, Elshenawy MM, Mason CE, Urathamakul T, Ozawa K, Robinson A, Goudsmits JM, Wang Y, Pan X, Beck JL, van Oijen AM, Huber T, Hamdan SM, Dixon NE (2013) A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode. EMBO J 32:1322–1333PubMedCentralCrossRefPubMedGoogle Scholar
  19. Kim DR, McHenry CS (1996a) Biotin tagging deletion analysis of domain limits involved in protein-macromolecular interactions: mapping the τ binding domain of the DNA polymerase III α subunit. J Biol Chem 271:20690–20698CrossRefPubMedGoogle Scholar
  20. Kim DR, McHenry CS (1996b) Identification of the β-binding domain of the α subunit of Escherichia coli polymerase III holoenzyme. J Biol Chem 271:20699–20704CrossRefPubMedGoogle Scholar
  21. Kim DR, Pritchard AE, McHenry CS (1997) Localization of the active site of the α subunit of the Escherichia coli DNA polymerase III holoenzyme. J Bacteriol 179:6721–6728PubMedCentralPubMedGoogle Scholar
  22. Lamers MH, Georgescu RE, Lee SG, O’Donnell M, Kuriyan J (2006) Crystal structure of the catalytic α subunit of E. coli replicative DNA polymerase III. Cell 126:881–892CrossRefPubMedGoogle Scholar
  23. Leu FP, Georgescu R, O’Donnell ME (2003) Mechanism of the E. coli τ processivity switch during lagging-strand synthesis. Mol Cell 11:315–327CrossRefPubMedGoogle Scholar
  24. Liu B, Lin J, Steitz TA (2013) Structure of the Pol III α-τ(c)-DNA complex suggests an atomic model of the replisome. Structure 21:658–664PubMedCentralCrossRefPubMedGoogle Scholar
  25. Maki H, Mo JY, Sekiguchi M (1991) A strong mutator effect caused by an amino acid change in the α subunit of DNA polymerase III of Escherichia coli. J Biol Chem 266:5055–5061PubMedGoogle Scholar
  26. Marceau AH, Bahng S, Massoni SC, George NP, Sandler SJ, Marians KJ, Keck JL (2011) Structure of the SSB-DNA polymerase III interface and its role in DNA replication. EMBO J 30:4236–4247PubMedCentralCrossRefPubMedGoogle Scholar
  27. McHenry CS (2011) DNA replicases from a bacterial perspective. Annu Rev Biochem 80:403–436CrossRefPubMedGoogle Scholar
  28. Nakane S, Nakagawa N, Kuramitsu S, Masui R (2009) Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3′–5′ exonuclease activity. Nucleic Acids Res 37:2037–2052PubMedCentralCrossRefPubMedGoogle Scholar
  29. Naue N, Fedorov R, Pich A, Manstein DJ, Curth U (2010) Site-directed mutagenesis of the χ subunit of DNA polymerase III and single-stranded DNA-binding protein of E. coli reveals key residues for their interaction. Nucleic Acids Res 39:1398–1407PubMedCentralCrossRefPubMedGoogle Scholar
  30. Oller AR, Schaaper R (1994) Spontaneous mutation in Escherichia coli containing the DnaE911 DNA polymerase antimutator allele. Genetics 138:263–270PubMedCentralPubMedGoogle Scholar
  31. Ozawa K, Horan NP, Robinson A, Yagi H, Hill FR, Jergic S, Xu ZQ, Loscha KV, Li N, Tehei M, Oakley AJ, Otting G, Huber T, Dixon NE (2013) Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits alpha, epsilon, theta and beta reveals a highly flexible arrangement of the proofreading domain. Nucleic Acids Res 41:5354–5367PubMedCentralCrossRefPubMedGoogle Scholar
  32. Pascal JM, O’Brien PJ, Tomkinson AE, Ellenberger T (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432:473–478CrossRefPubMedGoogle Scholar
  33. Pritchard AE, McHenry CS (1999) Identification of the acidic residues in the active site of DNA polymerase III. J Mol Biol 285:1067–1080CrossRefPubMedGoogle Scholar
  34. Reems JA, Wood S, McHenry CS (1995) Escherichia coli DNA polymerase III holoenzyme subunits α, β and γ directly contact the primer template. J Biol Chem 270:5606–5613CrossRefPubMedGoogle Scholar
  35. Sanders GM, Dallmann HG, McHenry CS (2010) Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases. Mol Cell 37:273–281CrossRefPubMedGoogle Scholar
  36. Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry 36:11205–11215CrossRefPubMedGoogle Scholar
  37. Shereda RD, Kozlov AG, Lohman TM, Cox MM, Keck JL (2008) SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 43:289–318PubMedCentralCrossRefPubMedGoogle Scholar
  38. Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O’Donnell M, Kuriyan J (2009) The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell 137:659–671PubMedCentralCrossRefPubMedGoogle Scholar
  39. Stano NM, Chen J, McHenry CS (2006) A coproofreading Zn(2+)-dependent exonuclease within a bacterial replicase. Nat Struct Mol Biol 13:458–459CrossRefPubMedGoogle Scholar
  40. Strauss BS, Roberts R, Francis L, Pouryazdanparast P (2000) Role of the dinB gene product in spontaneous mutation in Escherichia coli with an impaired replicative polymerase. J Bacteriol 182:6742–6750PubMedCentralCrossRefPubMedGoogle Scholar
  41. Su XC, Jergic S, Keniry MA, Dixon NE, Otting G (2007) Solution structure of domains IVa and V of the τ subunit of Escherichia coli DNA polymerase III and interaction with the α subunit. Nucleic Acids Res 35:2825–2832PubMedCentralCrossRefPubMedGoogle Scholar
  42. Teplyakov A, Obmolova G, Khil PP, Howard AJ, Camerini-Otero RD, Gilliland GL (2003) Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site. Proteins 51:315–318CrossRefPubMedGoogle Scholar
  43. Theobald DL, Mitton-Fry RM, Wuttke DS (2003) Nucleic acid recognition by OB-fold proteins. Annu Rev Biophys Biomol Struct 32:115–133PubMedCentralCrossRefPubMedGoogle Scholar
  44. Toste RA, Holding AN, Kent H, Lamers MH (2013) Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. EMBO J 32:1334–1343CrossRefGoogle Scholar
  45. Vandewiele D, Fernandez de Henestrosa AR, Timms AR, Bridges BA, Woodgate R (2002) Sequence analysis and phenotypes of five temperature sensitive mutator alleles of dnaE, encoding modified alpha-catalytic subunits of Escherichia coli DNA polymerase III holoenzyme. Mutat Res 499:85–95CrossRefPubMedGoogle Scholar
  46. Wieczorek A, McHenry CS (2006) The NH(2)-terminal php domain of the α subunit of the E. coli replicase binds the ε proofreading subunit. J Biol Chem 281:12561–12567CrossRefPubMedGoogle Scholar
  47. Wing RA (2010) Structural studies of the prokaryotic replisome. Thesis/Dissertation, Yale University, p 170Google Scholar
  48. Wing RA, Bailey S, Steitz TA (2008) Insights into the replisome from the structure of a ternary complex of the DNA polymerase III α-subunit. J Mol Biol 382:859–869PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Chemistry and BiochemistryUniversity of Colorado at BoulderBoulderUSA