Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin

Journal of Virology

Volumn 85, Issue 7, 2011, Pages 3621-3630

  Capodagli, Glenn C ^a   McKercher, Marissa A ^a   Baker, Erica A ^a   Masters, Emily M ^a   Brunzelle, Joseph S ^b   Pegan, Scott D ^a  

^a UNIVERSITY OF DENVER   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOMETHYLCOUMARIN; COUMARIN DERIVATIVE; INTERFERON STIMULATED GENE 15; NEDD8 PROTEIN; NUCLEIC ACID BINDING PROTEIN; PROTEINASE; UBIQUITIN; UBIQUITIN PROPYLAMINE; UNCLASSIFIED DRUG; VIRAL OVARIAN TUMOR DOMAIN PROTEASE;

AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; COVALENT BOND; CRYSTAL STRUCTURE; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; NAIRO VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; HEMORRHAGIC FEVER VIRUS, CRIMEAN-CONGO; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE HYDROLASES; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; SEQUENCE HOMOLOGY, AMINO ACID; UBIQUITIN; VIRAL PROTEINS;

CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS; IXODIDA; NAIROVIRUS;

EID: 79952613536     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02496-10     Document Type: Article

References (49)

1. Adams, P. D., et al. 2010. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66:213-221.
2. Al-Hakim, A. K., et al. 2008. Control of AMPK-related kinases by USP9X and atypical Lys(29)/Lys(33)-linked polyubiquitin chains. Biochem. J. 411:249-260.
3. Anagnostou, V., and A. Papa. 2009. Evolution of Crimean-Congo hemorrhagic fever virus. Infect. Genet. Evol. 9:948-954.
4. Arguello, M. D., and J. Hiscott. 2007. Ub surprised: viral ovarian tumor domain proteases remove ubiquitin and ISG15 conjugates. Cell Host Microbe 2:367-369. (Pubitemid 350215329)
5. Baker, N. A., D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U. S. A. 98:10037-10041.
6. Bergeron, E., C. G. Albarino, M. L. Khristova, and S. T. Nichol. 2010. Crimean-Congo hemorrhagic fever virus-encoded ovarian tumor protease activity is dispensable for virus RNA polymerase function. J. Virol. 84:216-226.
7. Chastagner, P., A. Israel, and C. Brou. 2006. Itch/AIP4 mediates Deltex degradation through the formation of K29-linked polyubiquitin chains. EMBO Rep. 7:1147-1153. (Pubitemid 44660572)
8. Clementz, M. A., et al. 2010. Deubiquitinating and interferon antagonism activities of coronavirus papain-like proteases. J. Virol. 84:4619-4629.
9. Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50:760-763.
10. Datta, A. B., G. L. Hura, and C. Wolberger. 2009. The structure and conformation of Lys63-linked tetraubiquitin. J. Mol. Biol. 392:1117-1124.
11. Duh, D., et al. 2008. The complete genome sequence of a Crimean-Congo hemorrhagic fever virus isolated from an endemic region in Kosovo. Virol. J. 5:7.
12. Edelmann, M. J., et al. 2009. Structural basis and specificity of human otubain 1-mediated deubiquitination. Biochem. J. 418:379-390.
13. Emsley, P., and K. Cowtan. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60:2126-2132.
14. Frias-Staheli, N., et al. 2007. Ovarian tumor domain-containing viral proteases evade ubiquitin- and ISG15-dependent innate immune responses. Cell Host Microbe 2:404-416. (Pubitemid 350225347)
15. Gill, S. C., and P. H. von Hippel. 1989. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:319-326.
16. Grosse-Kunstleve, R. W., and P. D. Adams. 2003. Substructure search procedures for macromolecular structures. Acta Crystallogr. D Biol. Crystallogr. 59:1966-1973.
17. Ha, B. H., and E. E. Kim. 2008. Structures of proteases for ubiquitin and ubiquitin-like modifiers. BMB Rep. 41:435-443.
18. Herrmann, J., L. O. Lerman, and A. Lerman. 2007. Ubiquitin and ubiquitin-like proteins in protein regulation. Circ. Res. 100:1276-1291.
19. Karti, S. S., et al. 2004. Crimean-Congo hemorrhagic fever in Turkey. Emerg. Infect. Dis. 10:1379-1384.
20. Kayagaki, N., et al. 2007. DUBA: a deubiquitinase that regulates type I interferon production. Science 318:1628-1632. (Pubitemid 350233662)
21. Komander, D., and D. Barford. 2008. Structure of the A20 OTU domain and mechanistic insights into deubiquitination. Biochem. J. 409:77-85.
22. Komander, D., M. J. Clague, and S. Urbe. 2009. Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10:550-563.
23. Lenschow, D. J., et al. 2007. IFN-stimulated gene 15 functions as a critical antiviral molecule against influenza, herpes, and Sindbis viruses. Proc. Natl. Acad. Sci. U. S. A. 104:1371-1376.
24. Lessel, U., and D. Schomburg. 1994. Similarities between protein 3-D structures. Protein Eng. 7:1175-1187. (Pubitemid 24319395)
25. McCoy, A. J., et al. 2007. Phaser crystallographic software. J. Appl. Crystallogr. 40:658-674.
26. Meissner, J. D., et al. 2006. A variable region in the Crimean-Congo hemorrhagic fever virus L segment distinguishes between strains isolated from different geographic regions. J. Med. Virol. 78:223-228.
27. Messick, T. E., et al. 2008. Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. J. Biol. Chem. 283:11038-11049.
28. Morikawa, S., M. Saijo, and I. Kurane. 2007. Recent progress in molecular biology of Crimean-Congo hemorrhagic fever. Comp. Immunol. Microbiol. Infect. Dis. 30:375-389.
29. Murshudov, G. N., A. A. Vagin, and E. J. Dodson. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53:240-255.
30. Nanao, M. H., et al. 2004. Crystal structure of human otubain 2. EMBO Rep. 5:783-788. (Pubitemid 39199167)
31. Otwinowski, Z., and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode, p. 307-326. In C. W. Carter, Jr., and R. M. Sweet (ed.), Macromolecular crystallography, vol. 276, part A. Academic Press, New York, NY. (Pubitemid 27085611)
32. Ozkaya, E., et al. 2010. Molecular epidemiology of Crimean-Congo hemorrhagic fever virus in Turkey: occurrence of local topotype. Virus Res. 149:64-70.
33. Pickart, C. M., and R. E. Cohen. 2004. Proteasomes and their kin: proteases in the machine age. Nat. Rev. Mol. Cell Biol. 5:177-187.
34. Sadler, A. J., and B. R. Williams. 2008. Interferon-inducible antiviral effectors. Nat. Rev. Immunol. 8:559-568.
35. Schlieker, C., et al. 2007. Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes. Mol. Cell 25:677-687. (Pubitemid 46341922)
36. Schrödinger, LLC. 2010. The AxPyMOL molecular graphics plugin for Microsoft PowerPoint, version 1.0. Schrödinger, LLC, Portland, OR. http: //www.pymol.org/ax.
37. Schrödinger, LLC. 2010. The JyMOL molecular graphics development component, version 1.0. Schrödinger, LLC, Portland, OR. http://www.pymol.org /jymol.
38. Schrödinger, LLC. 2010. The PyMOL molecular graphics system, version 1.3r1. Schrödinger, LLC, Portland, OR. http://www.pymol.org/pymol.
39. Snijder, E. J., A. L. Wassenaar, W. J. Spaan, and A. E. Gorbalenya. 1995. The arterivirus Nsp2 protease: an unusual cysteine protease with primary structure similarities to both papain-like and chymotrypsin-like proteases. J. Biol. Chem. 270:16671-16676.
40. Sun, L., and Z. J. Chen. 2004. The novel functions of ubiquitination in signaling. Curr. Opin. Cell Biol. 16:119-126.
41. Terwilliger, T. C., et al. 2009. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr. D Biol. Crystallogr. 65:582-601.
42. van Dijk, A. D., D. Fushman, and A. M. Bonvin. 2005. Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins 60:367-381.
43. Weber, F., and A. Mirazimi. 2008. Interferon and cytokine responses to Crimean Congo hemorrhagic fever virus; an emerging and neglected viral zonoosis. Cytokine Growth Factor Rev. 19:395-404.
44. Weeks, S. D., K. C. Grasty, L. Hernandez-Cuebas, and P. J. Loll. 2009. Crystal structures of Lys-63-linked tri- and di-ubiquitin reveal a highly extended chain architecture. Proteins 77:753-759.
45. Wilkinson, K. D., T. Gan-Erdene, and N. Kolli. 2005. Derivitization of the C-terminus of ubiquitin and ubiquitin-like proteins using intein chemistry: methods and uses. Methods Enzymol. 399:37-51. (Pubitemid 41772720)
46. World Health Organization. 2001. Crimean-Congo haemorrhagic fever, fact sheet no. 208. WHO Media Centre, World Health Organization, Geneva, Switzerland.
47. World Health Organization. 2003. Crimean-Congo haemorrhagic fever (CCHF) in Mauritania - update. World Health Organization, Geneva, Switzerland.
48. Zhao, C., C. Denison, J. M. Huibregtse, S. Gygi, and R. M. Krug. 2005. Human ISG15 conjugation targets both IFN-induced and constitutively expressed proteins functioning in diverse cellular pathways. Proc. Natl. Acad. Sci. U. S. A. 102:10200-10205.
49. Zhao, C., T. Y. Hsiang, R. L. Kuo, and R. M. Krug. 2010. ISG15 conjugation system targets the viral NS1 protein in influenza A virus-infected cells. Proc. Natl. Acad. Sci. U. S. A. 107:2253-2258.