XObserving a DNA polymerase choose right from wrong

Cell

Volumn 154, Issue 1, 2013, Pages 157-

  Freudenthal, Bret D ^a   Beard, William A ^a   Shock, David D ^a   Wilson, Samuel H ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; PYROPHOSPHATE;

ARTICLE; CATALYSIS; CHEMICAL REACTION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA DETERMINATION; DNA STRUCTURE; ESCHERICHIA COLI; GENE EXPRESSION; GENE INSERTION; GENOMIC INSTABILITY; METAL BINDING; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL;

EID: 84879897415     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.05.048     Document Type: Article

References (27)

1. P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.-W. Hung, G.J. Kapral, and R.W. Grosse-Kunstleve PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
2. V.K. Batra, W.A. Beard, D.D. Shock, J.M. Krahn, L.C. Pedersen, and S.H. Wilson Magnesium-induced assembly of a complete DNA polymerase catalytic complex Structure 14 2006 757 766
3. V.K. Batra, W.A. Beard, D.D. Shock, L.C. Pedersen, and S.H. Wilson Structures of DNA polymerase β with active-site mismatches suggest a transient abasic site intermediate during misincorporation Mol. Cell 30 2008 315 324
4. W.A. Beard, and S.H. Wilson Purification and domain-mapping of mammalian DNA polymerase beta Methods Enzymol. 262 1995 98 107
5. W.A. Beard, and S.H. Wilson Structure and mechanism of DNA polymerase β Chem. Rev. 106 2006 361 382
6. W.A. Beard, D.D. Shock, X.-P. Yang, S.F. DeLauder, and S.H. Wilson Loss of DNA polymerase β stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity J. Biol. Chem. 277 2002 8235 8242
7. W.A. Beard, D.D. Shock, V.K. Batra, L.C. Pedersen, and S.H. Wilson DNA polymerase β substrate specificity: side chain modulation of the "A-rule" J. Biol. Chem. 284 2009 31680 31689
8. L.S. Beese, and T.A. Steitz Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism EMBO J. 10 1991 25 33
9. M.A. Blasco, A. Bernad, L. Blanco, and M. Salas Characterization and mapping of the pyrophosphorolytic activity of the phage 29 DNA polymerase. Involvement of amino acid motifs highly conserved in α-like DNA polymerases J. Biol. Chem. 266 1991 7904 7909
10. K.-M. Chou, and Y.-C. Cheng An exonucleolytic activity of human apurinic/apyrimidinic endonuclease on 3′ mispaired DNA Nature 415 2002 655 659
11. E. Crespan, G. Maga, and U. Hübscher A new proofreading mechanism for lesion bypass by DNA polymerase-λ EMBO Rep. 13 2012 68 74
12. M.E. Dahlberg, and S.J. Benkovic Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant Biochemistry 30 1991 4835 4843
13. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
14. B.D. Freudenthal, W.A. Beard, and S.H. Wilson Structures of dNTP intermediate states during DNA polymerase active site assembly Structure 20 2012 1829 1837
15. J.W. Hanes, and K.A. Johnson A novel mechanism of selectivity against AZT by the human mitochondrial DNA polymerase Nucleic Acids Res. 35 2007 6973 6983
16. K.A. Johnson Role of induced fit in enzyme specificity: a molecular forward/reverse switch J. Biol. Chem. 283 2008 26297 26301
17. J.M. Krahn, W.A. Beard, and S.H. Wilson Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity Structure 12 2004 1823 1832
18. P. Lin, L.C. Pedersen, V.K. Batra, W.A. Beard, S.H. Wilson, and L.G. Pedersen Energy analysis of chemistry for correct insertion by DNA polymerase β Proc. Natl. Acad. Sci. USA 103 2006 13294 13299
19. K.E. McAuley-Hecht, G.A. Leonard, N.J. Gibson, J.B. Thomson, W.P. Watson, W.N. Hunter, and T. Brown Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs Biochemistry 33 1994 10266 10270
20. P.R. Meyer, S.E. Matsuura, A.G. So, and W.A. Scott Unblocking of chain-terminated primer by HIV-1 reverse transcriptase through a nucleotide-dependent mechanism Proc. Natl. Acad. Sci. USA 95 1998 13471 13476
21. T. Nakamura, Y. Zhao, Y. Yamagata, Y.J. Hua, and W. Yang Watching DNA polymerase η make a phosphodiester bond Nature 487 2012 196 201
22. Z. Otwinowski, and W. Minor Processsing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
23. S.S. Patel, I. Wong, and K.A. Johnson Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant Biochemistry 30 1991 511 525
24. M.R. Sawaya, R. Prasad, S.H. Wilson, J. Kraut, and H. Pelletier Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: evidence for an induced fit mechanism Biochemistry 36 1997 11205 11215
25. W.A. Beard, and S.H. Wilson Structural insights into the origins of DNA polymerase fidelity Structure 11 2003 489 496
26. D.K. Braithwaite, and J. Ito Compilation, alignment, and phylogenetic relationships of DNA polymerases Nucleic Acids Res. 21 1993 787 802
27. H. Ling, F. Boudsocq, R. Woodgate, and W. Yang Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication Cell 107 2001 91 102