The Ins and outs of viral RNA polymerase translocation

Journal of Molecular Biology

Volumn 426, Issue 7, 2014, Pages 1373-1376

  Boehr, David D ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA DIRECTED RNA POLYMERASE; RNA POLYMERASE; VIRUS RNA; DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE;

CATALYSIS; CONFORMATIONAL TRANSITION; ENZYME STRUCTURE; MOLECULAR DYNAMICS; NONHUMAN; NOTE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTON TRANSPORT; RNA TRANSPORT; X RAY CRYSTALLOGRAPHY; DNA RNA HYBRIDIZATION; HYDROGEN BOND; POLIOMYELITIS VIRUS; RNA REPLICATION; RNA VIRUS; VIRUS REPLICATION;

DNA-DIRECTED RNA POLYMERASES; PROTEIN STRUCTURE, SECONDARY; PROTEIN TRANSPORT; VIRAL PROTEINS;

EID: 84895920030     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.12.030     Document Type: Note

References (39)

1. K.K. Ng, J.J. Arnold, and C.E. Cameron Structure-function relationships among RNA-dependent RNA polymerases Curr Top Microbiol Immunol 320 2008 137 156
2. Y. Waheed, A. Bhatti, and M. Ashraf RNA dependent RNA polymerase of HCV: a potential target for the development of antiviral drugs Infect Genet Evol 14 2013 247 257
3. H. Malet, N. Masse, B. Selisko, J.L. Romette, K. Alvarez, and J.C. Guillemot et al. The flavivirus polymerase as a target for drug discovery Antiviral Res 80 2008 23 35
4. M. Vignuzzi, J.K. Stone, and R. Andino Ribavirin and lethal mutagenesis of poliovirus: molecular mechanisms, resistance and biological implications Virus Res 107 2005 173 181
5. D.L. Ollis, P. Brick, R. Hamlin, N.G. Xuong, and T.A. Steitz Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP Nature 313 1985 762 766
6. T.A. Steitz A mechanism for all polymerases Nature 391 1998 231 232
7. A.J. Berdis Mechanisms of DNA polymerases Chem Rev 109 2009 2862 2879
8. T.A. Steitz Visualizing polynucleotide polymerase machines at work EMBO J 25 2006 3458 3468
9. C. Ferrer-Orta, R. Agudo, E. Domingo, and N. Verdaguer Structural insights into replication initiation and elongation processes by the FMDV RNA-dependent RNA polymerase Curr Opin Struct Biol 19 2009 752 758
10. J. Lescar, and B. Canard RNA-dependent RNA polymerases from flaviviruses and Picornaviridae Curr Opin Struct Biol 19 2009 759 767
11. G.M. Cheetham, D. Jeruzalmi, and T.A. Steitz Structural basis for initiation of transcription from an RNA polymerase-promoter complex Nature 399 1999 80 83
12. Y.W. Yin, and T.A. Steitz Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase Science 298 2002 1387 1395
13. Y.W. Yin, and T.A. Steitz The structural mechanism of translocation and helicase activity in T7 RNA polymerase Cell 116 2004 393 404
14. Y. Li, S. Korolev, and G. Waksman Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation EMBO J 17 1998 7514 7525
15. A.A. Golosov, J.J. Warren, L.S. Beese, and M. Karplus The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis Structure 18 2010 83 93
16. J.L. Hansen, A.M. Long, and S.C. Schultz Structure of the RNA-dependent RNA polymerase of poliovirus Structure 5 1997 1109 1122
17. E.K. O'Reilly, and C.C. Kao Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure Virology 252 1998 287 303
18. D. Garriga, C. Ferrer-Orta, J. Querol-Audi, B. Oliva, and N. Verdaguer Role of motif B loop in allosteric regulation of RNA-dependent RNA polymerization activity J Mol Biol 425 2013 2279 2287
19. S.M. McDonald, Y.J. Tao, and J.T. Patton The ins and outs of four-tunneled Reoviridae RNA-dependent RNA polymerases Curr Opin Struct Biol 19 2009 775 782
20. P. Gong, M.G. Kortus, J.C. Nix, R.E. Davis, and O.B. Peersen Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts PLoS One 8 2013 e60272
21. M.G. Kortus, B.J. Kempf, K.G. Haworth, D.J. Barton, and O.B. Peersen A template RNA entry channel in the fingers domain of the poliovirus polymerase J Mol Biol 417 2012 263 278
22. P. Gong, and O.B. Peersen Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase Proc Natl Acad Sci U S A 107 2010 22505 22510
23. V. Svetlov, and E. Nudler Macromolecular micromovements: how RNA polymerase translocates Curr Opin Struct Biol 19 2009 701 707
24. M. Kireeva, M. Kashlev, and Z.F. Burton Translocation by multi-subunit RNA polymerases Biochim Biophys Acta 1799 2010 389 401
25. D. Temiakov, V. Patlan, M. Anikin, W.T. McAllister, S. Yokoyama, and D.G. Vassylyev Structural basis for substrate selection by t7 RNA polymerase Cell 116 2004 381 391
26. H.Y. Wang, T. Elston, A. Mogilner, and G. Oster Force generation in RNA polymerase Biophys J 74 1998 1186 1202
27. R. Landick Active-site dynamics in RNA polymerases Cell 116 2004 351 353
28. R. Guajardo, and R. Sousa A model for the mechanism of polymerase translocation J Mol Biol 265 1997 8 19
29. G. Bar-Nahum, V. Epshtein, A.E. Ruckenstein, R. Rafikov, A. Mustaev, and E. Nudler A ratchet mechanism of transcription elongation and its control Cell 120 2005 183 193
30. P.H. von Hippel An integrated model of the transcription complex in elongation, termination, and editing Science 281 1998 660 665
31. D. Wang, D.A. Bushnell, K.D. Westover, C.D. Kaplan, and R.D. Kornberg Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Cell 127 2006 941 954
32. C. Castro, E.D. Smidansky, J.J. Arnold, K.R. Maksimchuk, I. Moustafa, and A. Uchida et al. Nucleic acid polymerases use a general acid for nucleotidyl transfer Nat Struct Mol Biol 16 2009 212 218
33. X. Yang, E.D. Smidansky, K.R. Maksimchuk, D. Lum, J.L. Welch, and J.J. Arnold et al. Motif D of viral RNA-dependent RNA polymerases determines efficiency and fidelity of nucleotide addition Structure 29 2012 1519 1527
34. X. Yang, J.L. Welch, J.J. Arnold, and D.D. Boehr Long-range interaction networks in the function and fidelity of poliovirus RNA-dependent RNA polymerase studied by nuclear magnetic resonance Biochemistry 49 2010 9361 9371
35. I.M. Moustafa, H. Shen, B. Morton, C.M. Colina, and C.E. Cameron Molecular dynamics simulations of viral RNA-dependent RNA polymerases link conserved and correlated motions of functional elements to fidelity J Mol Biol 410 2011 159 181
36. J.M. Dahl, A.H. Mai, G.M. Cherf, N.N. Jetha, D.R. Garalde, and A. Marziali et al. Direct observation of translocation in individual DNA polymerase complexes J Biol Chem 287 2012 13407 13421
37. K.R. Lieberman, J.M. Dahl, A.H. Mai, M. Akeson, and H. Wang Dynamics of the translocation step measured in individual DNA polymerase complexes J Am Chem Soc 134 2012 18816 18823
38. M. Dangkulwanich, T. Ishibashi, S. Liu, M.L. Kireeva, L. Lubkowska, and M. Kashlev et al. Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism Elife 2 2013 e00971
39. J.P. Loria, R.B. Berlow, and E.D. Watt Characterization of enzyme motions by solution NMR relaxation dispersion Acc Chem Res 41 2008 214 221