1bpb › Citations

Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.

Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J
Science 264 1930-5 (1994)
Related entries: 1bpd, 1bpe, 2bpc

Cited: 256 times
EuropePMC logo PMID: 7516581

Abstract

Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.

Reviews - 1bpb mentioned but not cited (1)

  1. Structure and function relationships in mammalian DNA polymerases. Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Cell Mol Life Sci 77 35-59 (2020)

Articles - 1bpb mentioned but not cited (5)



Reviews citing this publication (42)

  1. Eukaryotic DNA polymerases. Hubscher U, Maga G, Spadari S. Annu Rev Biochem 71 133-163 (2002)
  2. Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure. O'Reilly EK, Kao CC. Virology 252 287-303 (1998)
  3. An open and closed case for all polymerases. Doublié S, Sawaya MR, Ellenberger T. Structure 7 R31-5 (1999)
  4. RNA-specific ribonucleotidyl transferases. Martin G, Keller W. RNA 13 1834-1849 (2007)
  5. The mechanism of action of T7 DNA polymerase. Doublié S, Ellenberger T. Curr Opin Struct Biol 8 704-712 (1998)
  6. The X family portrait: structural insights into biological functions of X family polymerases. Moon AF, Garcia-Diaz M, Batra VK, Beard WA, Bebenek K, Kunkel TA, Wilson SH, Pedersen LC. DNA Repair (Amst) 6 1709-1725 (2007)
  7. Polymerase structures and function: variations on a theme? Joyce CM, Steitz TA. J Bacteriol 177 6321-6329 (1995)
  8. Coordination of DNA single strand break repair. Abbotts R, Wilson DM. Free Radic Biol Med 107 228-244 (2017)
  9. Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase. Motea EA, Berdis AJ. Biochim Biophys Acta 1804 1151-1166 (2010)
  10. Structural and mechanistic relationships between nucleic acid polymerases. Sousa R. Trends Biochem Sci 21 186-190 (1996)
  11. DNA polymerase family X: function, structure, and cellular roles. Yamtich J, Sweasy JB. Biochim Biophys Acta 1804 1136-1150 (2010)
  12. DNA polymerase delta in DNA replication and genome maintenance. Prindle MJ, Loeb LA. Environ Mol Mutagen 53 666-682 (2012)
  13. The genomic enzymology of antibiotic resistance. Morar M, Wright GD. Annu Rev Genet 44 25-51 (2010)
  14. Base excision repair enzyme family portrait: integrating the structure and chemistry of an entire DNA repair pathway. Parikh SS, Mol CD, Tainer JA. Structure 5 1543-1550 (1997)
  15. The DNA-polymerase-X family: controllers of DNA quality? Ramadan K, Shevelev I, Hübscher U. Nat Rev Mol Cell Biol 5 1038-1043 (2004)
  16. Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template-primer. Ding J, Hughes SH, Arnold E. Biopolymers 44 125-138 (1997)
  17. DNA polymerases in the mitochondria: A critical review of the evidence. Krasich R, Copeland WC. Front Biosci (Landmark Ed) 22 692-709 (2017)
  18. Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates. Arnold E, Ding J, Hughes SH, Hostomsky Z. Curr Opin Struct Biol 5 27-38 (1995)
  19. DNA polymerase mu, a candidate hypermutase? Ruiz JF, Domínguez O, Laín de Lera T, Garcia-Díaz M, Bernad A, Blanco L. Philos Trans R Soc Lond B Biol Sci 356 99-109 (2001)
  20. Getting a grip: polymerases and their substrate complexes. Jäger J, Pata JD. Curr Opin Struct Biol 9 21-28 (1999)
  21. Protein methylation and DNA repair. Lake AN, Bedford MT. Mutat Res 618 91-101 (2007)
  22. Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site. Wu S, Beard WA, Pedersen LG, Wilson SH. Chem Rev 114 2759-2774 (2014)
  23. Base excision repair and design of small molecule inhibitors of human DNA polymerase β. Wilson SH, Beard WA, Shock DD, Batra VK, Cavanaugh NA, Prasad R, Hou EW, Liu Y, Asagoshi K, Horton JK, Stefanick DF, Kedar PS, Carrozza MJ, Masaoka A, Heacock ML. Cell Mol Life Sci 67 3633-3647 (2010)
  24. Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases. Steitz TA, Yin YW. Philos Trans R Soc Lond B Biol Sci 359 17-23 (2004)
  25. Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases. Tomita K, Yamashita S. Front Genet 5 36 (2014)
  26. Fractions to functions: RNA polymerase II thirty years later. Woychik NA. Cold Spring Harb Symp Quant Biol 63 311-317 (1998)
  27. DNA polymerases β and λ and their roles in cell. Belousova EA, Lavrik OI. DNA Repair (Amst) 29 112-126 (2015)
  28. Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion. Wang J, Konigsberg WH. Front Mol Biosci 9 824794 (2022)
  29. What is the orientation of DNA polymerases on their templates? Hughes SH, Hostomsky Z, Le Grice SF, Lentz K, Arnold E. J Virol 70 2679-2683 (1996)
  30. The World of Cyclic Dinucleotides in Bacterial Behavior. Aline Dias da P, Nathalia Marins de A, Gabriel Guarany de A, Robson Francisco de S, Cristiane Rodrigues G. Molecules 25 E2462 (2020)
  31. A model for DNA polymerase translocation: worm-like movement of DNA within the binding cleft. Wlassoff WA, Dymshits GM, Lavrik OI. FEBS Lett 390 6-9 (1996)
  32. Structural Maturation of HIV-1 Reverse Transcriptase-A Metamorphic Solution to Genomic Instability. London RE. Viruses 8 E260 (2016)
  33. New structural snapshots provide molecular insights into the mechanism of high fidelity DNA synthesis. Freudenthal BD, Beard WA, Wilson SH. DNA Repair (Amst) 32 3-9 (2015)
  34. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)
  35. History of DNA polymerase β X-ray crystallography. Whitaker AM, Freudenthal BD. DNA Repair (Amst) 93 102928 (2020)
  36. PCD/DCoH: more than a second molecular saddle. Kim JL, Burley SK. Structure 3 531-534 (1995)
  37. Structure and function of 2:1 DNA polymerase.DNA complexes. Tang KH, Tsai MD. J Cell Physiol 216 315-320 (2008)
  38. The Role of Natural Polymorphic Variants of DNA Polymerase β in DNA Repair. Kladova OA, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 2390 (2022)
  39. Beyond Triphosphates: Reagents and Methods for Chemical Oligophosphorylation. Shepard SM, Jessen HJ, Cummins CC. J Am Chem Soc 144 7517-7530 (2022)
  40. Family A and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions. Shanbhag V, Sachdev S, Flores JA, Modak MJ, Singh K. Biology (Basel) 7 E5 (2018)
  41. Reverse Transcription in the Saccharomyces cerevisiae Long-Terminal Repeat Retrotransposon Ty3. Rausch JW, Miller JT, Le Grice SF. Viruses 9 E44 (2017)
  42. PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy. Díaz-Talavera A, Montero-Conde C, Leandro-García LJ, Robledo M. Biomolecules 12 248 (2022)

Articles citing this publication (208)



Related citations provided by authors (2)

Quick links