Homology model of the dengue 2 virus NS3 protease: Putative interactions with both substrate and NS2B cofactor

Journal of General Virology

Volumn 80, Issue 5, 1999, Pages 1167-1177

  Brinkworth, Ross I ^a   Fairlie, David P ^a   Leung, Donmienne ^a   Young, Paul R ^a,b  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b ROYAL CHILDREN'S HOSPITAL   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMIC ACID; LYSINE; PROTEINASE; VIRUS ENZYME; ZINC ION;

AMINO ACID SEQUENCE; ARTICLE; DENGUE VIRUS; HEPATITIS C VIRUS; MOLECULAR MODEL; PRIORITY JOURNAL;

EID: 0032930982     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/0022-1317-80-5-1167     Document Type: Article

References (52)

1. Arias, C. F., Preugschat, F. & Strauss, J. H. (1993). Dengue 2 virus NS2B and NS3 form a stable complex that can cleave NS3 within the helicase domain. Virology 193, 888-899.
2. Bartenschlager, R., Ahlborn-Laake, L., Mous, J. & Jacobsen, H. (1994). Kinetic and structural analyses of hepatitis C virus polyprotein processing. Journal of Virology 68, 5045-5055.
3. Bazan, J. F. & Fletterick, R. J. (1989). Detection of a trypsin-like serine protease domain in flaviviruses and pestiviruses. Virology 171, 637-639.
4. Bazan, J. F. & Fletterick, R. J. (1990). Structural and catalytic models of trypsin-like viral proteases. Seminars in Virology 1, 311-322.
5. Biedrzycka, A., Cauchi, M. R., Bartholomeusz, A., Gorman, J. J. & Wright, P. J. (1987). Characterization of protease cleavage sites involved in the formation of the envelope glycoprotein and three non-structural proteins of dengue virus type 2, New Guinea C strain. Journal of General Virology 68, 1317-1326.
6. Butkiewicz, N. J., Wendel, M., Zhang, R., Jubin, R., Pichardo, J., Smith, E. B., Hart, A. M., Ingram, R., Durkin, J., Mui, P. W., Murray, M. G., Ramanathan, L. & Dasmahapatra, B. (1996). Enhancement of hepatitis C virus NS3 proteinase activity by association with NS4A-specific synthetic peptides: identification of sequence and critical residues of NS4A for the cofactor activity. Virology 225, 328-338.
7. Castle, E., Leidner, U., Nowak, T., Wengler, G. & Wengler, G. (1986). Primary structure of the West Nile flavivirus genome region coding for all nonstructural proteins. Virology 149, 10-26.
8. Chambers, T. J., Hahn, C. S., Galler, R. & Rice, C. M. (1990a). Flavivirus genome organization, expression, and replication. Annual Review of Microbiology 44, 649-688.
9. Chambers, T. J., Weir, R. C., Grakoui, A., McCourt, D. W., Bazan, J. F., Fletterick, R. J. & Rice, C. M. (1990b). Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein. Proceedings of the National Academy of Sciences, USA 87, 8898-8902.
10. Chambers, T. J., Nestorowicz, A., Amberg, S. M. & Rice, C. M. (1993). Mutagenesis of the yellow fever virus NS2B protein: effects on proteolytic processing, NS2B-NS3 complex formation, and viral replication. Journal of Virology 67, 6797-6807.
11. Choi, H.-K., Tong, L., Minor, W., Dumas, P., Boege, U., Rossmann, M. G. & Wengler, G. (1991). Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature 354, 37-43.
12. Choi, H.-K., Lu, G., Lee, S., Wengler, G. & Rossmann, M. G. (1997). Structure of Semliki Forest virus core protein. Proteins 27, 345-359.
13. Clum, S., Ebner, K. E. & Padmanabhan, R. (1997). Cotranslational membrane insertion of the serine proteinase precursor NS2B-NS3(Pro) of dengue virus type 2 is required for efficient in vitro processing and is mediated through the hydrophobic regions of NS2B. Journal of Biological Chemistry 272, 30715-30723.
14. De Francesco, R., Urbani, A., Nardi, M. C., Tomei, L., Steinkuhler, C. & Tramontano, A. (1996). A zinc binding site in viral serine proteinases. Biochemistry 35, 13282-13287.
15. Edwards, P. D. & Bernstein, P. R. (1994). Synthetic inhibitors of elastase. Medicinal Research Reviews 14, 127-194.
16. Fairlie, D. P., West, M. L. & Wong, A. K. (1998). Towards protein surface mimetics. Current Medicinal Chemistry 5, 29-62.
17. Falgout, B. & Markoff, L. (1995). Evidence that flavivirus NS1-NS2A cleavage is mediated by a membrane-bound host protease in the endoplasmic reticulum. Journal of Virology 69, 7232-7243.
18. Falgout, B., Pethel, M., Zhang, Y.-M. & Lai, C.-J. (1991). Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins. Journal of Virology 65, 2467-2475.
19. Falgout, B., Miller, R. H. & Lai, C.-J. (1993). Deletion analysis of dengue virus type 4 nonstructural protein NS2B: identification of a domain required for NS2B-NS3 protease activity. Journal of Virology 67, 2034-2042.
20. Fu, J., Tan, B.-H., Yap, E.-H., Chan, Y.-C. & Tan, Y. H. (1992). Full-length cDNA sequence of dengue type 1 virus (Singapore strain S275/90). Virology 188, 953-958.
21. Gorbalenya, A. E., Donchenko, A. P., Koonin, E. V. & Blinov, V. M. (1989). N-terminal domains of putative helicases of flavi- and pestiviruses may be serine proteases. Nucleic Acids Research 17, 3889-3897.
22. Grakoui, A., McCourt, D. W., Wychowski, C., Feinstone, S. M. & Rice, C. M. (1993). Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. Journal of Virology 67, 2832-2843.
23. Kim, J. L., Morgenstern, K. A., Lin, C., Fox, T., Dwyer, M. D., Landro, J. A., Chambers, S. P., Markland, W., Lepre, C. A., O'Malley, E. T., Harbeson, S. L., Rice, C. M., Murcko, M. A., Caron, P. R. & Thomson, J. A. (1996). Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87, 343-355.
24. Kyte, J. & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 157, 105-132.
25. Lin, C., Amberg, S. M., Chambers, T. J. & Rice, C. M. (1993). Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/4B signalase site. Journal of Virology 67, 2327-2335.
26. Lin, C., Thomson, J. A. & Rice, C. M. (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. Journal of Virology 69, 4373-4380.
27. Lobigs, M. (1993). Flavivirus premembrane protein cleavage and spike heterodimer secretion require the function of the viral proteinase NS3. Proceedings of the National Academy of Sciences, USA 90, 6218-6222.
28. Love, R. A., Parge, H. E., Wickersham, J. A., Hostomsky, Z., Habuka, N., Moomaw, E. W., Adachi, T. & Hostomska, Z. (1996). The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell 87, 331-342.
29. Love, R. A., Parge, H. E., Wickersham, J. A., Hostomsky, Z., Habuka, N., Moomaw, E. W., Adachi, T., Margosiak, S., Dagostino, E. & Hostomska, Z. (1998). The conformation of hepatitis C virus NS3 proteinase with and without NS4A: a structural basis for the activation of the enzyme by its cofactor. Clinical and Diagnostic Virology 10, 151-156.
30. Lüthy, R., Bowie, J. U. & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature 356, 83-85.
31. Mackow, E., Makino, Y., Zhao, B. T., Zhang, Y.-M., Markoff, L., Buckler-White, A., Guiler, M., Chanock, R. & Lai, C.-J. (1987). The nucleotide sequence of dengue type 4 virus : analysis of genes coding for nonstructural proteins. Virology 159, 217-228.
32. Nowak, T., Farber, P. M., Wengler, G. & Wengler, G. (1989). Analyses of the terminal sequences of West Nile virus structural proteins and of the in vitro translation of these proteins allow the proposal of a complete scheme of the proteolytic cleavages involved in their synthesis. Virology 169, 365-376.
33. Osatomi, K. & Sumiyoshi, H. (1990). Complete nucleotide sequence of dengue type 3 virus genome RNA. Virology 176, 643-647.
34. Parton, R. G. (1996). Caveolae and caveolins. Current Opinion in Cell Biology 8, 542-548.
35. Perona, J. J. & Craik, C. S. (1995). Structural basis of substrate specificity in the serine proteases. Protein Science 4, 337-360.
36. Preugschat, F., Yao, C.-W. & Strauss, J. H. (1990). In vitro processing of dengue virus type 2 nonstructural proteins NS2A, NS2B, and NS3. Journal of Virology 64, 4364-4374.
37. Preugschat, F., Lenches, E. M. & Strauss, J. H. (1991). Flavivirus enzyme-substrate interactions studied with chimeric proteinases: identification of an intragenic locus important for substrate recognition. Journal of Virology 65, 4749-4758.
38. Reid, R. C. & Fairlie, D. P. (1997). Mimicking extended conformations of protease substrates: designing cyclic peptidomimetics to inhibit HIV-1 protease. In Advances in Amino Acid Mimetics and Peptidomimetics, pp. 77-107. Edited by A. Abell. London: JAI Press.
39. Rice, C. M., Lenches, E. M., Eddy, S. R., Shin, S. J., Sheets, R. L. & Strauss, J. H. (1985). Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. Science 229, 726-733.
40. Rice, C. M., Aebersold, R., Teplow, D. B., Pata, J., Bell, J. R., Vorndam, A. V., Trent, D. W., Brandriss, M. W., Schlesinger, J. J. & Strauss, J. H. (1986). Partial N-terminal amino acid sequences of three nonstructural proteins of two flaviviruses. Virology 151, 1-9.
41. Rost, B., Casadio, R., Fariselli, P. & Sander, C. (1995). Transmembrane helices predicted at 95% accuracy. Protein Science 4, 521-533.
42. Ryan, M. D., Monaghan, S. & Flint, M. (1998). Virus-encoded proteinases of the Flaviviridae. Journal of General Virology 79, 947-959.
43. Speight, G., Coia, G., Parker, M. D. & Westaway, E. G. (1988). Gene mapping and positive identification of the non-structural proteins NS2A, NS2B, NS3, NS4B and NS5 of the flavivirus Kunjin and their cleavage sites. Journal of General Virology 69, 23-34.
44. Stadler, K., Allison, S. L, Schalich, J. & Heinz, F. X. (1997). Proteolytic activation of tick-borne encephalitis virus by furin. Journal of Virology 71, 8475-8481.
45. Sumiyoshi, H., Mori, C., Fuke, I., Morita, K., Kuhara, S., Kondou, J., Kikuchi, Y., Nagamatu, H. & Igarishi, A. (1987). Complete nucleotide sequence of the Japanese encephalitis virus genome RNA. Virology 161, 497-510.
46. 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. Journal of Virology 69, 1575-1581.
47. Teo, K. F. & Wright, P. J. (1997). Internal proteolysis of the NS3 protein specified by dengue virus 2. Journal of General Virology 78, 337-341.
48. Valle, R. P. C. & Falgout, B. (1998). Mutagenesis of the NS3 protease of dengue virus type 2. Journal of Virology 72, 624-632.
49. Wengler, G., Czaya, G., Färber, P. M. & Hegemann, J. H. (1991). In vitro synthesis of West Nile virus proteins indicates that the amino-terminal segment of the NS3 protein contains the active centre of the protease which cleaves the viral polyprotein after multiple basic amino acids. Journal of General Virology 72, 851-858.
50. Westaway, E. G., Mackenzie, J. M., Kenney, M. T., Jones, M. K. & Khromykh, A. A. (1997). Ultrastructure of Kunjin virus-infected cells: colocalization of NS1 and NS3 with double-stranded RNA, and of NS2B with NS3, in virus-induced membrane structures. Journal of Virology 71, 6650-6661.
51. World Health Organization (1996). Dengue and Dengue Haemorrhagic Fever. Report N117. Geneva: World Health Organization.
52. Yan, Y., Li, Y., Munshi, S., Sardana, V., Cole, J. L., Sardana, M., Steinkuehler, C., Tomei, L., De Francesco, R., Kuo, L. C. & Chen, Z. (1998). 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 7, 837-847.