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Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography.

Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA
J Mol Biol 381 529-39 (2008)
Cited: 39 times
EuropePMC logo PMID: 18614176

Abstract

Archaeal family B DNA polymerases bind tightly to template-strand uracil and stall replication on encountering the pro-mutagenic base. This article describes an X-ray crystal structure, at 2.8 A resolution, of Thermococcus gorgonarius polymerase in complex with a DNA primer-template containing uracil in the single-stranded region. The DNA backbone is distorted to position the uracil deeply within a pocket, located in the amino-terminal domain of the polymerase. Specificity arises from a combination of hydrogen bonds between the protein backbone and uracil, with the pocket shaped to prevent the stable binding of the four standard DNA bases. Strong interactions are seen with the two phosphates that flank the uracil and the structure gives clues concerning the coupling of uracil binding to the halting of replication. The importance of key amino acids, identified by the analysis of the structure and their conservation between archaeal polymerases, was confirmed by site-directed mutagenesis. The crystal structure of V93Q, a polymerase variant that no longer recognises uracil, is also reported, explaining the V93Q phenotype by the steric exclusion of uracil from the pocket.

Articles - 2vwk mentioned but not cited (1)

  1. An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion synthesis polymerases within the B family. Jozwiakowski SK, Keith BJ, Gilroy L, Doherty AJ, Connolly BA. Nucleic Acids Res 42 9949-9963 (2014)


Reviews citing this publication (9)

  1. The eukaryotic replicative DNA polymerases take shape. Johansson E, Macneill SA. Trends Biochem Sci 35 339-347 (2010)
  2. Replicative DNA polymerases. Johansson E, Dixon N. Cold Spring Harb Perspect Biol 5 a012799 (2013)
  3. DNA polymerases as useful reagents for biotechnology - the history of developmental research in the field. Ishino S, Ishino Y. Front Microbiol 5 465 (2014)
  4. Structural insights into eukaryotic DNA replication. Doublié S, Zahn KE. Front Microbiol 5 444 (2014)
  5. Antimutator variants of DNA polymerases. Herr AJ, Williams LN, Preston BD. Crit Rev Biochem Mol Biol 46 548-570 (2011)
  6. Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. Shin DS, Pratt AJ, Tainer JA. Archaea 2014 206735 (2014)
  7. Alteration of enzymes and their application to nucleic acid amplification (Review). Yasukawa K, Yanagihara I, Fujiwara S. Int J Mol Med 46 1633-1643 (2020)
  8. Archaeal DNA polymerases in biotechnology. Zhang L, Kang M, Xu J, Huang Y. Appl Microbiol Biotechnol 99 6585-6597 (2015)
  9. Direct Enzyme Engineering of B Family DNA Polymerases for Biotechnological Approaches. Kuznetsova AA, Kuznetsov NA. Bioengineering (Basel) 10 1150 (2023)

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  2. 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases. Klinge S, Núñez-Ramírez R, Llorca O, Pellegrini L. EMBO J 28 1978-1987 (2009)
  3. Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV. Biol Direct 4 11 (2009)
  4. Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis. Cubonová L, Richardson T, Burkhart BW, Kelman Z, Connolly BA, Reeve JN, Santangelo TJ. J Bacteriol 195 2322-2328 (2013)
  5. Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex. Wang M, Xia S, Blaha G, Steitz TA, Konigsberg WH, Wang J. Biochemistry 50 581-590 (2011)
  6. Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex. Mayanagi K, Kiyonari S, Nishida H, Saito M, Kohda D, Ishino Y, Shirai T, Morikawa K. Proc Natl Acad Sci U S A 108 1845-1849 (2011)
  7. Structures of KOD and 9°N DNA polymerases complexed with primer template duplex. Bergen K, Betz K, Welte W, Diederichs K, Marx A. Chembiochem 14 1058-1062 (2013)
  8. DNA polymerase preference determines PCR priming efficiency. Pan W, Byrne-Steele M, Wang C, Lu S, Clemmons S, Zahorchak RJ, Han J. BMC Biotechnol 14 10 (2014)
  9. Low-resolution structure of vaccinia virus DNA replication machinery. Sèle C, Gabel F, Gutsche I, Ivanov I, Burmeister WP, Iseni F, Tarbouriech N. J Virol 87 1679-1689 (2013)
  10. Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues. Killelea T, Ghosh S, Tan SS, Heslop P, Firbank SJ, Kool ET, Connolly BA. Biochemistry 49 5772-5781 (2010)
  11. Discovery and evolution of RNA and XNA reverse transcriptase function and fidelity. Houlihan G, Arangundy-Franklin S, Porebski BT, Subramanian N, Taylor AI, Holliger P. Nat Chem 12 683-690 (2020)
  12. Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase. Gouge J, Ralec C, Henneke G, Delarue M. J Mol Biol 423 315-336 (2012)
  13. Structures of an apo and a binary complex of an evolved archeal B family DNA polymerase capable of synthesising highly cy-dye labelled DNA. Wynne SA, Pinheiro VB, Holliger P, Leslie AG. PLoS One 8 e70892 (2013)
  14. Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme. Yan J, Beattie TR, Rojas AL, Schermerhorn K, Gristwood T, Trinidad JC, Albers SV, Roversi P, Gardner AF, Abrescia NGA, Bell SD. Nat Commun 8 15075 (2017)
  15. Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea. Emptage K, O'Neill R, Solovyova A, Connolly BA. J Mol Biol 383 762-771 (2008)
  16. DNA polymerase hybrids derived from the family-B enzymes of Pyrococcus furiosus and Thermococcus kodakarensis: improving performance in the polymerase chain reaction. Elshawadfy AM, Keith BJ, Ee Ooi H, Kinsman T, Heslop P, Connolly BA. Front Microbiol 5 224 (2014)
  17. Novel inhibition of archaeal family-D DNA polymerase by uracil. Richardson TT, Gilroy L, Ishino Y, Connolly BA, Henneke G. Nucleic Acids Res 41 4207-4218 (2013)
  18. Plasmid-based lacZalpha assay for DNA polymerase fidelity: application to archaeal family-B DNA polymerase. Jozwiakowski SK, Connolly BA. Nucleic Acids Res 37 e102 (2009)
  19. Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil. Richardson TT, Wu X, Keith BJ, Heslop P, Jones AC, Connolly BA. Nucleic Acids Res 41 2466-2478 (2013)
  20. The 3'-5' proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases. Russell HJ, Richardson TT, Emptage K, Connolly BA. Nucleic Acids Res 37 7603-7611 (2009)
  21. A modified family-B archaeal DNA polymerase with reverse transcriptase activity. Jozwiakowski SK, Connolly BA. Chembiochem 12 35-37 (2011)
  22. Compartmentalized self-replication (CSR) selection of Thermococcus litoralis Sh1B DNA polymerase for diminished uracil binding. Tubeleviciute A, Skirgaila R. Protein Eng Des Sel 23 589-597 (2010)
  23. Expanding the DNA alphabet in the fruit fly: uracil enrichment in genomic DNA. Horváth A, Békési A, Muha V, Erdélyi M, Vértessy BG. Fly (Austin) 7 23-27 (2013)
  24. Archaeoglobus Fulgidus DNA Polymerase D: A Zinc-Binding Protein Inhibited by Hypoxanthine and Uracil. Abellón-Ruiz J, Waldron KJ, Connolly BA. J Mol Biol 428 2805-2813 (2016)
  25. Production and characterisation of Epstein-Barr virus helicase-primase complex and its accessory protein BBLF2/3. Thierry E, Brennich M, Round A, Buisson M, Burmeister WP, Hutin S. Virus Genes 51 171-181 (2015)
  26. Archaeal DNA Polymerase-B as a DNA Template Guardian: Links between Polymerases and Base/Alternative Excision Repair Enzymes in Handling the Deaminated Bases Uracil and Hypoxanthine. Abellón-Ruiz J, Ishino S, Ishino Y, Connolly BA. Archaea 2016 1510938 (2016)
  27. DNA pol λ's extraordinary ability to stabilize misaligned DNA. Foley MC, Padow VA, Schlick T. J Am Chem Soc 132 13403-13416 (2010)
  28. Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase. Kropp HM, Ludmann S, Diederichs K, Betz K, Marx A. Chembiochem 22 3060-3066 (2021)
  29. Cooperative dynamics of a DNA polymerase replicating complex. Moors SL, Herdewijn P, Robben J, Ceulemans A. Biochim Biophys Acta 1834 2554-2563 (2013)


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