The modeled structure of the RNA dependent RNA polymerase of GBV-C virus suggests a role for motif E in Flaviviridae RNA polymerases

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Ferron, François ^a   Bussetta, Cécile ^a   Dutartre, Hélène ^a   Canard, Bruno ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BOVINE VIRAL DIARRHEA VIRUS; COMPARATIVE MODELING; EVOLUTIONARY RELATIONSHIPS; INITIATION MECHANISM; REPLICATION MECHANISM; REPLICATION PROCESS; RNA-DEPENDENT RNA POLYMERASE; SUBSTRATE-BINDING SITES;

BODY FLUIDS; COMPUTER SIMULATION; ENZYME ACTIVITY; PATHOGENS; POLYMERS; VIRUSES;

RNA;

ANTIVIRUS AGENT; GUANOSINE TRIPHOSPHATE; RNA DIRECTED RNA POLYMERASE; VIRUS ENZYME; VIRUS RNA;

ALLOSTERISM; ARTICLE; BOVINE DIARRHEA VIRUS; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; FLAVIVIRUS; HEPATITIS C VIRUS; HEPATITIS G VIRUS; MODEL; NONHUMAN; PHYLOGENY; PROTEIN FAMILY; PROTEIN MOTIF; RNA SYNTHESIS; STRUCTURAL BIOINFORMATICS; BINDING SITE; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; ENZYMOLOGY; GENETICS; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ANIMALIA; BOVINE VIRAL DIARRHEA VIRUS 1; FLAVIVIRIDAE; FLAVIVIRUS; GB VIRUS C/HEPATITIS G VIRUS; HEPATITIS C VIRUS;

BINDING SITES; GB VIRUS C; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RNA REPLICASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 27644591451     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-255     Document Type: Article

References (47)

1. Ranjith-Kumar, C.T., et al., De novo initiation pocket mutations have multiple effects on hepatitis C virus RNA-dependent RNA polymerase activities. J Virol, 2004. 78(22): p. 12207-17
2. World Health Organization. Global surveillance and control of hepatitis C. J Viral Hepatitis. 1999. 6 p. 35-47
3. Lindenbach, B.D. and C.M. Rice, Flaviridae : The viruses and their replication, in Fields virology, D.M. Knipe and P.M. Howley, Editors. 2001. p. 991-1042.
4. Kao, C.C., P. Singh, and D.J. Ecker, De novo initiation of viral RNA-dependent RNA synthesis. Virology, 2001. 287(2): p. 251-60.
5. Kao, C.C., A.M. Del Vecchio, and W. Zhong, De novo initiation of RNA synthesis by a recombinant flaviviridae RNA-dependent RNA polymerase. Virology, 1999. 253(1): p. 1-7.
6. Kim, M.J., et al., Template nucleotide moieties required for de novo initiation of RNA synthesis by a recombinant viral RNA-dependent RNA polymerase. J Virol, 2000. 74(22): p. 10312-22.
7. Luo, G., et al., De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus. J Virol, 2000. 74(2): p. 851-63.
8. Bressanelli, S., et al., Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides. J Virol, 2002. 76(7): p. 3482-92.
9. Adachi, T., et al., The essential role of C-terminal residues in regulating the activity of hepatitis C virus RNA-dependent RNA polymerase. Biochim Biophys Acta, 2002. 1601(1): p. 38-48.
10. Zhong, W., et al., RNA-dependent RNA polymerase activity encoded by GB virus-B non-structural protein 5B. J Viral Hepat, 2000. 7(5): p. 335-42.
11. Choi, K.H., et al., The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation. Proc Natl Acad Sci U S A, 2004. 101(13): p. 4425-30.
12. Muerhoff, A.S., et al., Genomic organization of GB viruses A and B: two new members of the Flaviviridae associated with GB agent hepatitis. J Virol, 1995. 69(9): p. 5621-30.
13. Simons, J.N., et al., Isolation of novel virus-like sequences associated with human hepatitis. Nat Med, 1995. 1(6): p. 564-9.
14. Ranjith-Kumar, C.T., et al., Requirements for de novo initiation of RNA synthesis by recombinant flaviviral RNA-dependent RNA polymerases. J Virol, 2002. 76(24): p. 12526-36.
15. Ranjith-Kumar, C.T., et al., Enzymatic activities of the GB virus-B RNA-dependent RNA polymerase. Virology, 2003. 312(2): p. 270-80.
16. Ferron, F., et al., VaZyMolO: A tool to define modularity in viral proteins. Journal of General Virology, 2005. 86(Pt3): p. 743-9
17. Altschul, S.F., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 1997. 25(17): p. 3389-402.
18. McGuffin, L.J., et al., The PSIPRED protein structure prediction server. Bioinformatics, 2000. 16(4): p. 404-5.
19. Canutescu AA, Shelenkov AA, Dunbrack RL Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 2003 Sep; 12(9):2001-14.
20. Bates, P.A., et al., Enhancement of Protein Modelling by Human Intervention in Applying the Automatic Programs 3D-JIGSAW and 3D-PSSM. Proteins: Structure, Function and Genetics, 2001. Suppl 5:39-46
21. Bates, P.A. and Sternberg, M.J.E. Model Building by Comparison at CASP3: Using Expert Knowledge and Computer Automation. Proteins: Structure, Function and Genetics, 1999. Suppl 3:47-54
22. Contreras-Moreira,B., et al., Domain Fishing: a first step in protein comparative modelling. Bioinformatics, 2002. 18: 1141-1142.
23. Fiser A, and Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol, 2003. 374:461-491.
24. Eisenberg D, et al., VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol., 1997. 277:396-404
25. Laskowski R A, et al., PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst, 1993. 26: p. 283-291.
26. Vriend, G., WHAT IF: a molecular modeling and drug design program. J Mol Graph, 1990. 8(1): p. 52-6, 29.
27. Lyle, J.M., et al., Visualization and functional analysis of RNA-dependent RNA polymerase lattices. Science, 2002. 296(5576): p. 2218-22.
28. Qin, W., et al., Oligomeric interaction of hepatitis C virus NS5B is critical for catalytic activity of RNA-dependent RNA polymerase. J Biol Chem, 2002. 277(3): p. 2132-7.
29. Dutartre, H., et al., A relaxed discrimination of 2′-O-methyl GTP relative to GTP between de novo and elongative RNA synthesis by the hepatitis C RNA-dependent RNA polymerase NS5B. J Biol Chem, 2005. 280(8): p. 6359-68
30. Bairoch, A. and R. Apweiler, The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res, 2000. 28(1): p. 45-8.
31. Berman, H.M., et al., The Protein Data Bank. Nucleic Acids Res, 2000. 28(1): p. 235-42.
32. Thompson, J.D., D.G. Higgins, and T.J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 1994. 22(22): p. 4673-80.
33. Galtier, N., M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci, 1996. 12(6): p. 543-8.
34. Ginalski K, et al., 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, (2003) May 22;19(8):1015-8.
35. Cuff, J.A. and G.J. Barton, Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 2000. 40(3): p. 502-11.
36. Rost, B., PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol, 1996. 266: p. 525-39.
37. Gouet, P., et al., ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics, 1999. 15(4): p. 305-8.
38. Gouet, P. and E. Courcelle, ENDscript: a workflow to display sequence and structure information. Bioinformatics, 2002. 18(5): p. 767-8.
39. Esnouf, R.M., An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model, 1997. 15(2): p. 132-4, 112-3.
40. Guex, N. and M.C. Peitsch, SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 1997. 18(15): p. 2714-23.
41. Gunsteren, W.F.v. and B. H.J.C, Computer Simulation of Molecular Dynamics: Methodology, Applications and Perspectives in Chemistry, in Angew. Chem. Int., E. Engl., Editor. 1990. p. 992-1023.
42. Gunsteren, W.F.v., et al., Computer simulation of protein motion. Computer Phys. Communications, 1995. 91: p. 305-319.
43. Sharp, K., Fine, R., and Honig, B, Computer simulations of the diffusion of a substrate to an active site of an enzyme. Science, 1987. 236: p. 1460-1463.
44. Roussel, A. and C. Cambillau, TURBO-FRODO, M.V. Silicon Graphics, CA, Editor. 1991, In Silicon Graphics Geometry Partners Directory,. p. 86.
45. Morris, G.M., et al., "Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function". Journal of Computational Chemistry, 1998. 19: p. 1639-1662.
46. Wallace, A.C., et al., LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng, 1995. 8(2): p. 127-34.
47. Ago, H., et al., Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Structure Fold Des, 1999. 7(11): p. 1417-26.