The nsp9 Replicase Protein of SARS-Coronavirus, Structure and Functional Insights

Structure

Volumn 12, Issue 2, 2004, Pages 341-353

  Sutton, Geoff ^a   Fry, Elizabeth ^a   Carter, Lester ^a   Sainsbury, Sarah ^a   Walter, Tom ^a   Nettleship, Joanne ^a   Berrow, Nick ^a   Owens, Ray ^a   Gilbert, Robert ^a   Davidson, Andrew ^b   Siddell, Stuart ^b   Poon, Leo L M ^c   Diprose, Jonathan ^a   Alderton, David ^a   Walsh, Martin ^d   Grimes, Jonathan M ^a   Stuart, David I ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

^d EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; NON STRUCTURAL PROTEIN 8; NON STRUCTURAL PROTEIN 9; SERINE PROTEINASE; UNCLASSIFIED DRUG; VIRUS PROTEIN; VIRUS RNA;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CORONAVIRUS; CRYSTAL STRUCTURE; ENZYME STRUCTURE; LIGHT SCATTERING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INTERACTION; RNA SYNTHESIS; SEVERE ACUTE RESPIRATORY SYNDROME; STRUCTURE ANALYSIS; ULTRACENTRIFUGATION;

CORONAVIRUS; RNA VIRUSES; SARS CORONAVIRUS; SARS COV;

EID: 10744222104     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.01.016     Document Type: Article

References (51)

1. Altamirano M.M., Woolfson A., Donda A., Shamshiev A., Briseno-Roa L., Foster N.W., Veprintsev D.B., De Libero G., Fersht A.R., Milstein C. Ligand-independent assembly of recombinant human CD1 by using oxidative refolding chromatography. Proc. Natl. Acad. Sci. USA. 98:2001;2950-2952.
2. Anand K., Palm G.J., Mesters J.R., Siddell S.G., Ziebuhr J., Hilgenfeld R. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α-helical domain. EMBO J. 21:2002;3213-3224.
3. pro) structure. basis for design of anti-SARS drugs Science. 300:2003;1763-1767.
4. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
5. Bordier C. Phase separation of integral membrane proteins in Triton X-114 solution. J. Biol. Chem. 256:1981;1604-1607.
6. Bost A.G., Carnahan R.H., Tao Lu X., Denison M.R. Four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly. J. Virol. 74:1999;3379-3387.
7. Brockway S.M., Clay C.T., Lu X.T., Denison M.R. Characterization of the expression, intracellular localization, and replication complex associated with the putative mouse hepatitis virus RNA-dependent RNA polymerase. J. Virol. 77:2003;10515-10527.
8. Brown J., Walter T.S., Carter L., Abrescia N.G.A., Ariescu A.R., Batuwangala T.D., Bird L.E., Brown N., Chamberlain P.P., Davis S.J.et al. A procedure for setting up high-throughput nanolitre crystallization experiments. II. Crystallization results. J. Appl. Crystallogr. 36:2003;315-318.
9. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography and NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
10. Burley S.K. An overview of structural genomics. Nat. Struct. Biol. Suppl. 7:2000;932-934.
11. Byron O. Construction of hydrodynamic bead models from high resolution X-ray crystallographic or nuclear magnetic resonance data. Biophys. J. 72:1997;408-415.
12. Campanacci V., Egloff M.-P., Longhi S., Ferron F., Rancurel C., Salomoni A., Durousseau C., Tocque F., Bremond N., Dobbe J.C.et al. Structural genomics of the SARS coronavirus. cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein Acta Crystallogr. D Biol. Crystallogr. 59:2003;1628-1631.
13. CCP4 The CCP4 suite. programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50:1994;760-763.
14. Donnelly C.A., Ghani A.C., Leung G.M., Hedley A.J., Fraser C., Riley S., Abu-Raddad L.J., Ho L.M., Thach T.Q., Chau P.et al. Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong. Lancet. 361:2003;1761-1766.
15. Dunker A.K., Brown C.J., Lawson J.D., Iakoucheva L.M., Obradovic Z. Intrinsic disorder and protein function. Biochemistry. 41:2002;6573-6582.
16. Egger D., Teterina N., Ehrenfeld E., Bienz K. Formation of the poliovirus replication complex requires coupled viral translation, vesicle production and viral RNA synthesis. J. Virol. 74:2000;6570-6580.
17. Esnouf R.M. An extensively modified version of MolScript which includes greatly enhanced coloring capabilities. J. Mol. Graph. 15:1997;132-134.
18. Garcia de la Torre J., Harding S.E., Carrasco B. Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program. Eur. Biophys. J. 28:1999;119-132.
19. Gouet P., Courcelle E., Stuart D.I., Metoz F. ESPript. multiple sequence alignments in Postscript Bioinformatics. 15:1999;305-308.
20. Ikemizu S., Gilbert R.J.C., Fennelly J.A., Collins A.V., Harlos K., Jones E.Y., Stuart D.I., Davis S.J. Structure and dimerization of a soluble form of B7-1. Immunity. 12:2000;51-60.
21. Jones T.A., Zou Y.-J., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
22. Kuiken T., Fouchier R.A., Schutten M., Rimmelzwaan G.F., van Amerongen G., van Riel D., Laman J.D., de Jong T., van Doornum G., Lim W.et al. Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome. Lancet. 362:2003;263-270.
23. Lawrence M.C., Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234:1993;946-950.
24. Marra M.A., Jones S.J., Astell C.R., Holt R.A., Brooks-Wilson A., Butterfield Y.S., Khattra J., Asano J.K., Barber S.A., Chan S.Y.et al. The genome sequence of the SARS-associated coronavirus. Science. 300:2003;1399-1404.
25. Merrit E.A., Murphy M.E.P. Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 50:1994;869-873.
26. Merry A.H., Gilbert R.J.C., Shore D.A., Royle L., Miroshnychenko M.V., Wormald M.R., Harvey D.J., Dwek R.A., Classon B.J., Rudd P.M.et al. o-glycan sialylation and the structure of the stalk-like region of the T cell co-receptor CD8. J. Biol. Chem. 278:2003;27119-27128.
27. Murzin A.G. OB (oligonucleotide/oligosaccharide binding)-fold. common structural and functional solution for non-homologous sequences EMBO J. 12:1993;861-867.
28. Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.
29. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
30. Pasternak A.O., van den Born E., Spaan W.J., Snijder E.J. Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis. EMBO J. 20:2001;7220-7228.
31. Peiris J.S., Chu C.M., Cheng V.C., Chan K.S., Hung I.F., Poon L.L., Law K.I., Tang B.S., Hon T.Y., Chan C.S.et al. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia. a prospective study Lancet. 361:2003;1767-1772.
32. Rota P.A., Oberste M.S., Monroe S.S., Nix W.A., Campagnoli R., Icenogle J.P., Penaranda S., Bankamp B., Maher K., Chen M.H.et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 300:2003;1394-1399.
33. Sawicki D., Wang T., Sawicki S. The RNA structures engaged in replication and transcription of the A59 strain of mouse hepatitis virus. J. Gen. Virol. 82:2001;385-396.
34. Schuck P., Rossmanith P. Determination of the sedimentation coefficient distribution by least-squares boundary modeling. Biopolymers. 54:2000;328-341.
35. Sethna P.B., Brian D.A. Coronavirus genomic and sub-genomic minus-strand RNAs copartition in membrane-protected replication complexes. J. Virol. 71:1997;7744-7749.
36. Siddell S., Sawicki D., Meyer Y., Thiel V., Sawicki S. Identification of the mutations responsible for the phenotype of three MHV RNA-negative ts mutants. Adv. Exp. Med. Biol. 494:2001;453-458.
37. Snijder E.J., Bredenbeek P.J., Dobbe J.C., Thiel V., Ziebuhr J., Poon L.L., Guan Y., Rozanov M., Spaan W.J., Gorbalenya A.E. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J. Mol. Biol. 331:2003;991-1004.
38. Stafford W.F.I. Boundary analysis in sedimentation transport experiments. a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile Anal. Biochem. 203:1992;295-301.
39. Stuart D.I., Levine M., Muirhead H., Stammers D.K. Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6Å J. Mol. Biol. 134:1979;109-142.
40. Tani H., Kamidate T., Watanabe H. Aqueous micellar two-phase systems for protein separation. Anal. Sci. 14:1998;875-888.
41. Terwilliger T.C. Maximum likelihood density modification. Acta Crystallogr. D Biol. Crystallogr. 56:2000;965-972.
42. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55:1999;849-861.
43. Theobald D.L., Mitton-Fry R.M., Wuttke D.S. Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct. 32:2003;115-133.
44. Thiel V., Ivanov K.A., Putics A., Hertzig T., Schelle B., Bayer S., Weissbrich B., Snijder E.J., Rabenau H., Doerr H.W.et al. Mechanisms and enzymes involved in SARS coronavirus genome expression. J. Gen. Virol. 84:2003;2305-2315.
45. Thompson J.D., Higgins D.G., Gibson T.J. Clustal W. improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22:1994;4673-4680.
46. Walker P.A., Leong L.E.-C., Porter A.G. Sequence and structural determinants of the interaction between the 5′-noncoding region of picornavirus RNA and rhinovirus protease 3C. J. Biol. Chem. 270:1995;14510- 14516.
47. Walter T.S., Diprose J., Brown J., Pickford M., Owens R.J., Stuart D.I., Harlos K. A procedure for setting up high-throughput nanolitre crystallization experiments. I. Protocol design and validation. J. Appl. Crystallogr. 36:2003;308-314.
48. Yang H., Yang M., Ding Y., Liu Y., Lou Z., Zhou Z., Sun L., Mo L., Ye S., Pang H.et al. The Crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc. Natl. Acad. Sci. USA. 100:2003;13190-13195.
49. Zeng F.Y., Chan C.W., Chan M.N., Chen J.D., Chow K.Y., Hon C.C., Hui K.H., Li J., Li V.Y., Wang C.Y.et al. The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39). Exp. Biol. Med. (Maywood). 228:2003;866-873.
50. Ziebuhr, J., and Siddell, S. (2002). Nidovirales. In The Encyclopaedia of Life Sciences (London: Stockton Press), pp. 190-198.
51. Ziebuhr J., Snijder E.J., Gorbalenya A.E. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J. Gen. Virol. 81:2000;853-879.