Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: A 2.2 Å resolution structure in a hexagonal crystal form

Protein Science

Volumn 7, Issue 4, 1998, Pages 837-847

  Yan, Youwei ^a   Ying, L I ^a   Munshi, Sanjeev ^a   Sardana, Vinod ^a   Cole, James L ^a   Sardana, Mohinder ^a   Steinkuehler, Christian ^b   Tomei, Licia ^b   De Francesco, Raffaele ^b   Kuo, Lawrence C ^a   Chen, Zhongguo ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

^b IRBM   (Italy)

Author keywords

Hepatitis C virus; NS3 protease; NS4A peptide; Serine protease; X ray structure

Indexed keywords

CHYMOTRYPSIN; PEPTIDE; PROTEINASE; SERINE PROTEINASE;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME STRUCTURE; HEPATITIS C VIRUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; X RAY CRYSTALLOGRAPHY;

HEPATITIS C VIRUS;

EID: 2642590958     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070402     Document Type: Article

References (50)

1. Bartenschlager R, Ahlborn-Laake L, Mous J, Jacobsen H. 1993. Nonstructural protein 3 of the hepatitis C virus encodes a serine-type proteinase required for cleavage at the NS3/4 and NS4/5 junctions. J Virol 67:3835-3844.
2. Bartenschlager R, Ahlborn-Laake L, Mous J, Jacobsen H. 1994. Kinetic and structural analyses of hepatitis C virus polyprotein processing. J Virol 68:5045-5055.
3. Bisceglie AM. 1995. Hepatitis C and hepatocellular carcinoma. Semin Liver Dis 15:64-69.
4. Blevins RA, Tulinsky A. 1985. The refinement and the structure of the dimer of a-chymotrypsin at 1.67Å resolution. J Biol Chem 200:4264-4275.
5. Blow DM. 1976. Structure and mechanism of chymotrypsin. Acc Chem Res 9:145-152.
6. Brünger AT. 1992. Free R value: A novel statistical quantity for assessing the accuracy of crystal structure. Nature 355:472-475.
7. Brünger AT. 1993. X-PLOR: A system for X-ray crystallography and NMR. New Haven. Connecticut: Yale University Press.
8. Carson M. 1991. Ribbons 2.0. J Appl Crystallogr 24:958-961.
9. Chen P, Tsuge H, Almassy RJ, Grihskov CL, Katoh S, Vanderpool DL, Margosiak SA, Pinko C, Matthews DA, Kan CC. 1996. Structure of the human cytomegalovirus protease catalytic domain reveals a novel serine protease fold and catalytic triad. Cell 86:835-843.
10. Choo Q-L, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M. 1989. Isolation of a cDNA clone derived from a blood-borne non-A non-B viral hepatitis genome. Science 244:359-362.
11. DeFrancesco R, Urbani A, Nardi MC, Tomei L, Steinkuehler C, Tramontano A. 1996. A zinc binding site in viral serine proteases. Biochemistry 35:13282-13287.
12. Eckart MR, Selby M, Masiarz F, Lee C, Berger K, Crawford K, Kuo C, Kuo G, Houghton M, Choo Q-L. 1993. The hepatitis C virus encodes a serine protease involved in the processing of the putative nonstructural proteins from the viral polyprotein precursor. Biochem Biophys Res Commun 192:399-406.
13. Failla C, Tomei L, De Francesco R. 1994. Both NS3 and NS4A are required for proteolytic processing of hepatitis C virus nonstructural proteins. J Virol 68:3753-3760.
14. Furey W, Swaminathan S. 1997. PHASES-95: A program package for the processing and analysis of diffraction data from macromolecules. Methods in Entymology 277:590-620.
15. Grakoui A, Wychowski C, Lin C, Feinstone SM, Rice CM. 1993. Expression and identification of hepatitis C virus polyprotein cleavage products. J Virol 67:1385-1395.
16. Harrison SC. 1996. Peptide-surface association: The case of PDZ and PTB domains. Cell 86:341-343.
17. Hijikata M, Kato N, Ootsuyama Y, Nakagawa M, Shimotohno K. 1991. Gene mapping of the putative structural region of the hepatitis C virus. Proc Natl Acad Sci USA 88:5547-5551.
18. Hijikata M, Mizushima H, Akagi T, Mon S, Kakiuchi N, Kato N, Tanaka T, Kimura K, Shimotohno K. 1993a. Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus. J Virol 67:4665-4675.
19. Hijikata M, Mizushima H, Tanji Y, Komoda Y, Hirowatari Y, Akagi T, Kato N, Kimura K, Shimotohno K. 1993b. Proteolytic processing and membrane association of putative nonstructural proteins of hepatitis C virus. Proc Natl Acad Sci USA 90:10773-10777.
20. Houghton M. 1996. Hepatitis C viruses. In: Fields BN, Knipe DM, Howley PM, eds. Fields virology. 3rd ed. New York: Raven Press. pp 1035-1058.
21. Huber R, Bode W. 1978. Structure basis of the activation and action of trypsin. Acc Chem Res 11:114-122.
22. Kleywegt GJ, Brünger AT. 1996. Checking your imagination: Applications of the free R value. Structure 4:897-904.
23. Kim JL, Morgenstern KA, Lin C, Fox T, Dwyer MD, Landro JA, Chamber, SP, Markland W, Lapre CA, O'melley ET, Harbeson SL, Rice CM, Murco MA, Caron PR, Thomso, JA. 1996. Crystal structure of the hepatitis C Virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87:343-355.
24. Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
25. Kuo G, Choo Q-L, Alter HJ, Gitnick GL, Redeker AG, Purcell RH, Miyamura T, Dienstag JL, Alter MJ, Stevens CE, Tagtmeier GE, Bonino F, Colombo M, Lee WS, Kuo C, Berger K, Shister JR, Overby LR, Bradley DW, Houghton M. 1989. An assay for circulating antibodies to a major etiologic virus of human non-A non-B hepatitis. Science 244:362-364.
26. Laskowski RA, Mac-Arthur MW, Moss DS, Thornton JM. 1993. PROCHECK: A program to check the stereochcmical quality of protein structures. J Appl Crystallogr 26:283-291.
27. Liddington RC, Yan Y, Moulai J, Sahli R, Benjamin TL, Harrison SC. 1991. Structure of simian virus 40 at 3.8 Å resolution. Nature 354:278-284.
28. Lin C, Pragai BM. Grakoui A, Xu J, Rice CM. 1994. Hepatitis C virus NS3 serine proteinase: Trans-cleavage requirements and processing kinetics. J Virol 65:8147-8157.
29. Lin C, Thomson JA, Rice CM. 1995. A central region in the hepatitis C virus NS4A protein allows formation of an active NS3-NS4A serine proteinase complex in vivo and in vitro. J Virol 67:4373-4380.
30. Love RA, Parge HE, Wickersham JA, Hostomsky Z, Habuka N, Moomaw EW, Adachi T, Hostomska Z. 1996. The crystal structure of the hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell 87:331-342.
31. Lovejoy B, Choe S, Cascio D, McRorie DK, DeGrado WF, Eisenberg D. 1993. Crystal structure of a synthetic triple-stranded α-helical bundle. Science 259:1288-1293.
32. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
33. Qiu X, Culp JS, Dilella AG, Hellmig B, Hoog SS, Janson CA, Smith WW, Abbel-Meguid SS. 1996. Unique fold and active site in cytomegalovirus protease. Nature 383:275-279.
34. Rice CM, Strauss EG, Strauss JH. 1986. In: Schlesinger S, Schlesinger MJ, eds. Togaviridae and Flaviviridae. New York: Plenum Press. pp 279-326.
35. Rost B, Casadio R, Fariselli P, Sander C. 1995. Transmembrane helices predicted at 95% accuracy. Protein Sci 4:521-533.
36. Sack JS. 1988. CHAIN: A crystallographic modeling program. Mol Graphics 6:224-225.
37. Saito I, Miyamura T, Obayashi A, Harada H, Katayama T, Kikuchi S, Watanabe Y, Koi S, Onji M, Ohata Y, Choo Q-L, Houghton M, Kuo G. 1990. Hepatitis C virus infection is associated with the development of hepatocellular carcinoma. Proc Natl Acad Sci USA 87:6547-6549.
38. Sheldrick GM. 1991. Heavy atom location using SHELXS-90. In: Wolf W, Evans PR, Leslie AGW, eds. Isomorphous replacement and anomalous scattering. Warrington, UK: SERC Daresbury Laboratory. Proceedings of the CCP4 study weekend 25-26 January 1991. pp 23-28.
39. Shieh HS, Kurumbail RG, Stevens AM, Stegeman RA, Sturman EJ, Pak JY, Wittwer AJ, Palmier MA, Wiegand RC, Holwerda BC, Stallings WC. 1996. Three-dimensional structure of human cytomegalovirus protease. Nature 389:279-282.
40. Shimizu Y, Kamaji K, Masuho Y, Yokota T, Inoue H, Sudo K, Satoh S, Shimotohno K. 1996. Identification of the sequence on NS4A required for enhanced cleavage of the NS5A/5B site by hepatitis C virus NS3 protease. J Virol 70:127-132.
41. Takamizawa A, Mori C, Fuke I, Mannabe S, Murakami S, Fujita J, Onoshi E, Andoh T, Yoshida I, Okayama H. 1991. Structure and organization of the hepatitis C virus genome isolated from human carriers. J Virol 65:1105-1113.
42. Tanji Y, Hijikata M, Satoh S, Kaneko T, Shimotohno K. 1995. Hepatitis C virus-encoded nonstructural protein NS4A has versatile functions in viral protein processing. J Virol 69:1575-1581.
43. Terwilliger TC, Eisenberg D. 1983. Unbiased three-dimensional refinement of heavy-atom parameters by correlation of origin-removed Patterson functions. Acta crystallogr A39:813-817.
44. Tomei L, Failla C, Santolini E, De Francesco R, La Monica N. 1993. NS3 is a serine protease required for processing hepatitis C virus polyprotein. J Virol 67:4017-4026.
45. Tomei L, Failla C, Vitale RL, Bianchi E, De Francesco R. 1996. A central hydrophobic domain of the hepatitis C virus NS4A protein is necessary and sufficient for the activation of the NS3 protease. J Gen Virol 77:1065-1070.
46. Tong L, Wengler G, Rossman MG. 1993. Refined structure of Sindbis virus core protein and comparison with other chymotrypsin-like serine proteinase structures. J Mol Biol 230:228-247.
47. Tong L, Qian C, Massariol MJ, Bonneau PR, Cordingley MG, Lagace L. 1996. A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease. Nature 383:272-275.
48. Yan Y, Winograd E, Viel A, Cronin T, Harrison SC, Branton D. 1993. Crystal structure of the repetitive segments of spectrin. Science 262:2027-2030.
49. Yan Y, Stehle T, Liddington RC, Zhao H, Harrison SC. 1995. Structure determination of simian virus 40 and murine polyomavirus by a combination of 30-fold and 5-fold electron-density averaging. Structure 4:157-164.
50. 21-34 complex at 2.8 Å resolution. Proceedings of the 4th International Meeting on Hepatitis C Virus and Related Viruses, Kyoto, Japan. p 8.