Nucleotide channel of RNA-dependent RNA polymerase used for intermolecular uridylylation of protein primer

Journal of Molecular Biology

Volumn 357, Issue 2, 2006, Pages 665-675

  Tellez, Andres B ^a   Crowder, Scott ^a   Spagnolo, Jeannie F ^a   Thompson, Aaron A ^b   Peersen, Olve B ^b   Brutlag, Douglas L ^a   Kirkegaard, Karla ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

Docking; Molecular dynamics; Polymerase; Protein priming; RNA replication

Indexed keywords

NUCLEOTIDE; PRIMER RNA; RNA DIRECTED RNA POLYMERASE; URIDINE PHOSPHATE; VIRUS PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL ANALYSIS; EXPERIMENTATION; GENETICS; MOLECULAR DYNAMICS; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; REACTION ANALYSIS;

POLIOVIRUS;

EID: 33344464455     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.12.044     Document Type: Article

References (33)

1. A.V. Paul, J.H. van Boom, D. Filippov, and E. Wimmer Protein-primed RNA synthesis by purified poliovirus RNA polymerase Nature 393 1998 280 284
2. R.R. Rueckert Picornaviridae and their replication B.N. Fields Virology 1995 Raven Press New York 609 654
3. A.V. Paul, J. Yin, J. Mugavero, E. Rieder, Y. Liu, and E. Wimmer A "slide-back" mechanism for the initiation of protein-primed RNA synthesis by the RNA polymerase of poliovirus J. Biol. Chem. 278 2003 43951 43960
4. L.S. Beese, V. Derbyshire, and T.A. Steitz Structure of DNA polymerase I Klenow fragment bound to duplex DNA Science 260 1993 352 355
5. J.M. Lyle, A. Clewell, K. Richmond, O.C. Richards, D.A. Hope, S.C. Schultz, and K. Kirkegaard Similar structural basis for membrane localization and protein priming by an RNA-dependent RNA polymerase J. Biol. Chem. 277 2002 16324 16331
6. J.S. Towner, T.V. Ho, and B.L. Semler Determinants of membrane association for poliovirus protein 3AB J. Biol. Chem. 271 1996 26810 26818
7. G.M.T. Cheetham, and T.A. Steitz Structure of a transcribing T7 RNA polymerase initiation complex Science 286 1999 2305 2309
8. H. Huang, R. Chopra, G.L. Verdine, and S.C. Harrison Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance Science 282 1998 1669 1675
9. J. Jager, and J.D. Pata Getting a grip: polymerases and their substrate complexes Curr. Opin. Struct. Biol. 9 1999 21 28
10. C. Ferrer-Orta, A. Arias, R. Perez-Luque, C. Escarmis, E. Domingo, and N. Verdaguer Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA J. Biol. Chem. 279 2004 47212 47221
11. J.E. Boerner, J.M. Lyle, S. Daijogo, B.L. Semler, S.C. Schultz, K. Kirkegaard, and O.C. Richards Allosteric effects of ligands and mutations on poliovirus RNA-dependent RNA polymerase J. Virol. 79 2005 7803 7811
12. R. Chen, and Z. Weng Docking unbound proteins using shape complementarity, desolvation, and electrostatics Proteins: Struct. Funct. Genet. 47 2002 281 294
13. N. Budin, N. Majeux, and A. Caflisch Fragment-based flexible ligand docking by evolutionary optimization Biol. Chem. 382 2001 1365 1372
14. M. Rarey, B. Kramer, T. Lengauer, and G. Klebe A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 261 1996 470 489
15. E. Lindahl, B. Hess, D. van der Spoel, and R. van Drunen GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Mod. 7 2001 302 317
16. A.A. Thompson, and O.B. Peersen Structural basis for proteolysis- dependent activation of the poliovirus RNA-dependent RNA polymerase EMBO J. 23 2004 3462 3471
17. J.L. Hansen, A.M. Long, and S.C. Schultz Structure of the RNA-dependent RNA polymerase of poliovirus Structure 5 1997 1109 1122
18. L. Jin, and J.A. Wells Dissecting the energetics of an antibody-antigen interface by alanine shaving and molecular grafting Protein Sci. 3 1994 2351 2357
19. J.A. Wells Binding in the growth hormone receptor complex Proc. Natl Acad. Sci. USA 93 1996 1 6
20. W. Xiang, A. Cuconati, A.V. Paul, X. Cao, and E. Wimmer Molecular dissection of the multifunctional poliovirus RNA-binding protein 3AB Rna 1 1995 892 904
21. A. Fersht Enzyme Structure and Mechanism 1984 W.H. Freeman Co. New York
22. T.C. Appleby, H. Luecke, J.H. Shim, J.Z. Wu, I.W. Cheney, and W. Zhong Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer J. Virol. 79 2005 277 288
23. S.D. Hobson, E.S. Rosenblum, O.C. Richards, K. Richmond, K. Kirkegaard, and S.C. Schultz Oligomeric structures of poliovirus polymerase are important for function EMBO J. 20 2001 1153 1163
24. H.B. Pathak, S.K. Ghosh, A.W. Roberts, S.D. Sharma, J.D. Yoder, and J.J. Arnold Structure-function relationships of the RNA-dependent RNA polymerase from poliovirus (3Dpol). A surface of the primary oligomerization domain functions in capsid precursor processing and VPg uridylylation J. Biol. Chem. 277 2002 31551 31562
25. J.M. Lyle, E. Bullitt, K. Bienz, and K. Kirkegaard Visualization and functional analysis of RNA-dependent RNA polymerase lattices Science 296 2002 2218 2222
26. N.M. Crawford, and D. Baltimore Genome-linked protein VPg of poliovirus is present as free VPg and VPg-pUpU in poliovirus-infected cells Proc. Natl Acad. Sci. USA 80 1983 7452 7455
27. K.T. Simmons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J. Mol. Biol. 268 1997 209 225
28. C. Bystroff, and Y. Shao Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA Bioinformatics 18 2002 S54 S61
29. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
30. A.A. Canutescu, A.A. Shelenkov, and R.L. Dunbrack Jr A graph theory algorithm for protein side-chain prediction Protein Sci. 12 2003 2001 2014
31. H.J.C. Berendsen, D. van der Spoel, and R. van Drunen GROMACS: a message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 91 1995 43 56
32. D.A. Hope, S.E. Diamond, and K. Kirkegaard Genetic dissection of interaction between poliovirus 3D polymerase and viral protein 3AB J. Virol. 71 1997 9490 9498
33. R.A. Love, K.A. Maegley, X. Yu, R.A. Ferre, L.K. Lingardo, and W. Diehl The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy Structure 12 2004 1533 1544