Structure-based mutagenesis study of hepatitis C virus NS3 helicase

Journal of Virology

Volumn 73, Issue 10, 1999, Pages 8798-8807

  Lin, Chao ^a   Kim, Joseph L ^a  

^a VERTEX PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ALANINE; LEUCINE; OLIGONUCLEOTIDE; PHENYLALANINE; POLYCYTIDYLIC ACID; POLYNUCLEOTIDE; POLYURIDYLIC ACID; RNA HELICASE; SERINE; SERINE PROTEINASE; THREONINE; TRYPTOPHAN; VIRUS PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CRYSTAL STRUCTURE; DNA DENATURATION; ENZYME ACTIVITY; ENZYME STRUCTURE; GENETIC CONSERVATION; HEPATITIS C VIRUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA BINDING; SITE DIRECTED MUTAGENESIS; X RAY CRYSTALLOGRAPHY;

EID: 0032824138     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.10.8798-8807.1999     Document Type: Article

References (48)

1. Bilderback, T., T. Fulmer, W. W. Mantulin, and M. Glaser. 1996. Substrate binding causes movement in the ATP binding domain of Escherichia coli adenylate kinase. Biochemistry 35:6100-6106.
2. Bryant, G. L., M. S. Harris, E. T. Baldwin, L. Tandeske, K. R. Shoemaker, and B. C. Finzel. 1999. HCV helicase RNA-binding-domain flexibility quantified by comparison of multiple crystal forms, p. 83. 1999, Annual American Crystallographic Association Meeting, Buffalo, N.Y.
3. Cho, H.-S., N.-C. Ha, L.-W. Kang, K. M. Chung, S. H. Back, S. K. Jang, and B.-H. Oh. 1998. Crystal structure of RNA helicase from genotype 1b hepatitis C virus. J. Biol. Chem. 273:15045-15052.
4. Choo, Q.-L., G. Kuo, A. J. Weiner, L. R. Overby, D. W. Bradley, and M. Houghton. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244:359-362.
5. Ellis, N. A. 1997. DNA helicases in inherited human disorders. Curr. Opin. Genet. Dev. 7:354-363.
6. Gorbalenya, A. E., and E. V. Koonin. 1993. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3:419-429.
7. Grakoui, A., D. W. McCourt, C. Wychowski, S. M. Feinstone, and C. M. Rice. 1993. Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. J. Virol. 67:2832-2843.
8. Grakoui, A., D. W. McCourt, C. Wychowski, S. M. Feinstone, and C. M. Rice. 1993. A second hepatitis C virus-encoded proteinase. Proc. Natl. Acad. Sci. USA 90:10583-10587.
9. Grakoui, A., C. Wychowski, C. Lin, S. M. Feinstone, and C. M. Rice. 1993. Expression and identification of hepatitis C virus polyprotein cleavage products. J. Virol. 67:1385-1395.
10. Gwack, Y., D. W. Kim, J. H. Han, and J. Choe. 1996. Characterization of RNA binding activity and RNA helicase activity of the hepatitis C virus NS3 protein. Biochem. Biophys. Res. Commun. 225:654-659.
11. Hakansson, K., A. J. Doherty, S. Shuman, and D. B. Wigley. 1997. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell 89:545-553.
12. Hong, Z., E. Ferrari, J. Wright-Minogue, R. Chase, C. Risano, G. Seelig, C.-G. Lee, and A. D. Kwong. 1996. Enzymatic characterization of hepatitis C virus NS3/4A complexes expressed in mammalian cells by using the herpes simplex virus amplicon system. J. Virol. 70:4261-4268.
13. Honghton, M. 1996. Hepatitis C viruses, p. 1035-1058. In B. N. Fields, D. M. Knipe, and P. M. Howley (ed.), Virology, 3rd ed. Raven Press, New York, N.Y.
14. Jin, L., and D. L. Peterson. 1995. Expression, isolation, and characterization of the hepatitis C virus ATPase/RNA helicase. Arch. Biochem. Biophys. 323:47-53.
15. Jones, P. S. 1998. Strategies for antiviral drug discovery. Antivir. Chem. Chemother. 9:283-302.
16. Kadaré, G., and A.-L. Haenni. 1997. Virus-encoded RNA helicases. J. Virol. 71:2583-2590.
17. Kanal, A., K. Tanabe, and M. Kohara. 1995. Poly (U) binding activity of hepatitis C virus NS3 protein, a putative RNA helicase. FEBS Lett. 376:221-224.
18. Kim, D. W., Y. Gwack, J. H. Han, and J. Choe. 1995. C-terminal domain of the hepatitis C virus NS3 protein contains an RNA helicase activity. Biochem. Biophys. Res. Commun. 215:150-166.
19. Kim, D. W., J. Kim, Y. Gwack, J. H. Han, and J. Choe. 1997. Mutational analysis of the hepatitis C virus RNA helicase. J. Virol. 71:9400-9409.
20. Kim, J. L., K. A. Morgenstern, J. P. Griffith, M. D. Dwyer, J. A. Thomson, M. A. Murcko, C. Lin, and P. R. Caron. 1998. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure 6:89-100.
21. Koonin, E. V., and V. V. Dolja. 1993. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit. Rev. Biochem. Mol. Biol. 28:375-430. (Erratum, 28:546.)
22. Korolev, S., J. Hsieh, G. H. Gauss, T. M. Lohman, and G. Waksman. 1997. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90:635-647.
23. Kunkel, T. A. 1985. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82:488-492.
24. Kuo, G., Q.-L. Choo, H. J. Alter, G. L. Gitnick, A. G. Redeker, R. H. Purcell, T. Miyamura, J. L. Dienstag, M. J. Alter, C. E. Stevens, G. E. Tegtmeier, F. Bonino, M. Colombo, W.-S. Lee, C. Kuo, K. Berger, J. R. Shuster, L. R. Overby, D. W. Bradley, and M. Houghton. 1989. An assay for circulating antibodies to a major etiologic virus of human non-A non-B hepatitis. Science 244:362-364.
25. Lin, C. Unpublished data.
26. Lin, C., T. J. Chambers, and C. M. Rice. 1993. Mutagenesis of conserved residues at the yellow fever virus 3/4A and 4B/5 dibasic cleavage sites: effects on cleavage efficiency and polyprotein processing. Virology 192:596-604.
27. Lin, C., B. D. Lindenbach, B. M. Prágai, D. W. McCourt, and C. M. Rice. 1994. Processing in the hepatitis C virus E2-NS2 region: identification of p7 and two distinct E2-specific products with different C termini. J. Virol. 68:5063-5073.
28. Lin, C., B. M. Prágai, A. Grakoui, J. Xu, and C. M. Rice. 1994. Hepatitis C virus NS3 serine proteinase: trans-cleavage requirements and processing kinetics. J. Virol. 68:8147-8157.
29. Liuzzi, M., J. J. Crute, C. A. Grygon, K. D. Hargrave, B. Simoneau, A.-M. Faucher, G. Bolger, J. Duan, P. Kibler, and M. G. Cordingley. 1998. Aminothiazolyl-phenyl-based inhibitors of HSV helicase-primase: a novel class of orally active antiherpetic agents. Antivir. Res. 37:A42.
30. Lohman, T. M., and K. P. Bjornson. 1996. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65:169-214.
31. Lüking, A., U. Stahl, and U. Schmidt. 1998. The protein family of RNA helicases. Crit. Rev. Biochem. Mol. Biol. 33:259-296.
32. Matson, S. W., D.W. Bean, and J. W. George. 1994. DNA helicases: enzymes with essential roles in all aspects of DNA metabolism. Bioessays 16:13-22.
33. Morgenstern, K. A., J. A. Landro, K. Hsiao, C. Lin, G. Yong, M. S.-S. Su, and J. A. Thomson. 1997. Polynucleotide modulation of the protease, nucleoside triphosphatase, and helicase activities of a hepatitis C virus NS3-NS4A complex isolated from transfected COS cells. J. Virol. 71:3767-3775.
34. Pause, A., N. Methot, and N. Sonenberg. 1993. The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis. Mol. Cell. Biol. 13:6789-6798.
35. Pause, A., and N. Sonenberg. 1992. Mutational analysis of a DEAD box RNA helicase: the mammalian translation initiation factor eIF-4A. EMBO J. 11:2643-2654.
36. 2, and poly(rU). Two ADP binding sites on the enzyme-nucleic acid complex. J. Biol. Chem. 273:7390-7396.
37. Porter, D. J. 1998. A kinetic analysis of the oligonucleotide-modulated ATPase activity of the helicase domain of the NS3 protein from hepatitis C virus. The first cycle of interaction of ATP with the enzyme is unique. J. Biol. Chem. 273:14247-14253.
38. Porter, D. J., S. A. Short, M. H. Hanlon, F. Preugschat, J. E. Wilson, D. H. Willard, Jr., and T. G. Consler. 1998. Product release is the major contributor to kcat for the hepatitis C virus helicase-catalyzed strand separation of short duplex DNA. J. Biol. Chem. 273:18906-18914.
39. Prengschat, F., D. R. Averett, B. E. Clarke, and D. J. T. Porter. 1996. A steady-state and pre-steady-state kinetic analysis of the NTPase activity associated with the hepatitis C virus NS3 helicase domain. J. Biol. Chem. 271:24449-24457.
40. Rice, C. M. 1996. Flaviviridae: the viruses and their replication, p. 931-960. In B. N. Fields, D. M. Knipe, and P. M. Howley (ed.), Virology, 3rd ed. Raven Press, New York, N.Y.
41. Schulz, G. E. 1992. Induced-fit movement in adenylate kinases. Faraday Discuss. 93:85-93.
42. Spector, F. C., L. Liang, H. Giordano, M. Sivaraja, and M. G. Peterson. 1998. Inhibition of herpes simplex virus replication by a 2-amino thiazole via interactions with the helicase component of the UL5-UL8-UL52 complex. J. Virol. 72:6979-6987.
43. Spector, F. C., L. Liang, H. Giordano, M. Sivaraja, and M. G. Peterson. 1998. T157602, a 2-amino-thiazole inhibits HSV replication by interacting with the UL5 component of the UL5/8/52 helicase primase complex. Antivir. Res. 37:A43.
44. Subramanya, H. S., L. E. Bird, J. A. Brannigan, and D. B. Wigley. 1996. Crystal structure of a DExx box DNA helicase. Nature 384:379-383.
45. Suzich, J. A., J. K. Tamura, F. Palmer-Hill, P. Warrener, A. Grakoui, C. M. Rice, S. M. Feinstone, and M. S. Collett. 1993. Hepatitis C virus NS3 protein polynucleotide-stimulated nucleoside triphosphatase and comparison with the related pestivirus and flavivirus enzymes. J. Virol. 67:6152-6158.
46. Tai, C-L., W.-K. Chi, D.-S. Chen, and L.-H. Hwang. 1996. The helicase activity associated with hepatitis C virus nonstructural protein 3 (NS3). J. Virol. 70:8477-8484.
47. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
48. Yao, N., T. Hesson, M. Cable, Z. Hong, A. D. Kwong, H. V. Le, and P. C. Weber. 1997. Structure of the hepatitis C virus RNA helicase domain. Nat. Struct. Biol. 4:463-467.