Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket

Virology

Volumn 346, Issue 2, 2006, Pages 440-451

  Gayathri, P ^a   Satheshkumar, P S ^a   Prasad, K ^a   Nair, Smita ^a   Savithri, H S ^a   Murthy, M R N ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Crystal structure; Glutamate specific protease; MIRAS; Polyprotein processing; S1 binding pocket; Serine protease; Sesbania mosaic virus; Trypsin fold

Indexed keywords

ALANINE; AROMATIC AMINO ACID; GLUTAMIC ACID; PROTEIN VPG; SERINE PROTEINASE; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ANIMAL CELL; ARTICLE; CRYSTAL STRUCTURE; MOSAIC VIRUS; MUTATIONAL ANALYSIS; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; SESBANIA MOSAIC VIRUS;

AMINO ACID SUBSTITUTION; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA MUTATIONAL ANALYSIS; MODELS, MOLECULAR; MOSAIC VIRUSES; MUTAGENESIS, SITE-DIRECTED; POLYPROTEINS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; SERINE ENDOPEPTIDASES; VIRAL PROTEINS; VIRUSES;

ANIMALIA; SESBANIA MOSAIC VIRUS;

EID: 33644824351     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2005.11.011     Document Type: Article

References (34)

1. I.H. Barrette-Ng, K.K. Ng, B.L. Mark, D. Van Aken, M.M. Cherney, C. Garen, Y. Kolodenko, A.E. Gorbalenya, E.J. Snijder, and M.N. James Structure of arterivirus nsp4. The smallest chymotrypsin-like proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole J. Biol. Chem. 277 1994 39960 39966
2. C.S. Bond TopDraw: a sketchpad for protein structure topology cartoons Bioinformatics 19 2 2003 311 312
3. CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr., D: Biol. Crystallogr. 50 1994 760 763
4. R. De Francesco, A. Urbani, M.C. Nardi, L. Tomei, C. Steinkuhler, and A. Tramontano A zinc binding site in viral serine proteinases Biochemistry 35 41 1996 13282 13287
5. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 Pt. 12 Pt. 1 2004 2126 2132
6. R.M. Esnouf Further additions to MolScript version 1.4, including reading and contouring of electron-density maps Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 Pt. 4 1999 938 940
7. A.E. Gorbalenya, E.V. Koonin, V.M. Blinov, and A.P. Donchenko Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picornaviruses FEBS Lett. 236 2 1988 287 290
8. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1 1993 123 138
9. L.A. Ivanoff, T. Towatari, J. Ray, B.D. Korant, and S.R. Petteway Jr. Expression and site-specific mutagenesis of the poliovirus 3C protease in Escherichia coli Proc. Natl. Acad. Sci. U.S.A. 83 15 1986 5392 5396
10. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24 1991 946 950
11. S. Kriminski, C.L. Caylor, M.C. Nonato, K.D. Finkelstein, and R.E. Thorne Flash-cooling and annealing of protein crystals Acta Crystallogr., Sect. D: Biol. Crystallogr. 58 Pt. 3 2002 459 471
12. G.L. Lokesh, K. Gopinath, P.S. Satheshkumar, and H.S. Savithri Complete nucleotide sequence of Sesbania mosaic virus: a new virus species of the genus Sobemovirus Arch. Virol. 146 2 2001 209 223
13. B.W. Matthews Solvent content of protein crystals J. Mol. Biol. 33 2 1968 491 497
14. R. Meijers, E.V. Blagova, V.M. Levdikov, G.N. Rudenskaya, G.G. Chestukhina, T.V. Akimkina, S.V. Kostrov, V.S. Lamzin, and I.P. Kuranova The crystal structure of glutamyl endopeptidase from Bacillus intermedius reveals a structural link between zymogen activation and charge compensation Biochemistry 43 10 2004 2784 2791
15. E.A. Merritt, and M.E. Murphy Raster3D Version 2.0. A program for photorealistic molecular graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 Pt. 6 1994 869 873
16. R.J. Morris, A. Perrakis, and V.S. Lamzin ARP/wARP and automatic interpretation of protein electron density maps Methods Enzymol. 374 2003 229 244
17. S.C. Mosimann, M.M. Cherney, S. Sia, S. Plotch, and M.N. James Refined X-ray crystallographic structure of the poliovirus 3C gene product J. Mol. Biol. 273 5 1997 1032 1047
18. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr., Sect. D: Biol. Crystallogr. 53 Pt. 3 1997 240 255
19. V.L. Nienaber, K. Breddam, and J.J. Birktoft A glutamic acid specific serine protease utilizes a novel histidine triad in substrate binding Biochemistry 32 43 1993 11469 11475
20. C.M. Nunn, M. Jeeves, M.J. Cliff, G.T. Urquhart, R.R. George, L.H. Chao, Y. Tscuchia, and S. Djordjevic Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site J. Mol. Biol. 350 2005 145 155
21. Z.M.W. Otwinowsky Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
22. J.J. Perona, and C.S. Craik Structural basis of substrate specificity in the serine proteases Protein Sci. 4 3 1995 337 360
23. J.F. Petersen, M.M. Cherney, H.D. Liebig, T. Skern, E. Kuechler, and M.N. James The structure of the 2A proteinase from a common cold virus: a proteinase responsible for the shut-off of host-cell protein synthesis EMBO J. 18 20 1999 5463 5475
24. J. Phan, A. Zdanov, A.G. Evdokimov, J.E. Tropea, H.K. Peters III, R.B. Kapust, M. Li, A. Wlodawer, and D.S. Waugh Structural basis for the substrate specificity of tobacco etch virus protease J. Biol. Chem. 277 52 2002 50564 50572
25. R.J. Read, M. Fujinaga, A.R. Sielecki, and M.N. James Structure of the complex of Streptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8-A resolution Biochemistry 22 19 1983 4420 4433
26. R.J. Read, and M.N. James Refined crystal structure of Streptomyces griseus trypsin at 1.7 A resolution J. Mol. Biol. 200 3 1988 523 551
27. P.S. Satheshkumar, G.L. Lokesh, and H.S. Savithri Polyprotein processing: cis and trans proteolytic activities of Sesbania mosaic virus serine protease Virology 318 1 2004 429 438
28. P.S. Satheshkumar, P. Gayathri, K. Prasad, and H.S. Savithri "Natively Unfolded" VPg is essential for Sesbania mosaic virus serine protease activity J. Biol. Chem. 280 34 2005 30291 30300
29. K. Sivakumaran, B.C. Fowler, and D.L. Hacker Identification of viral genes required for cell-to-cell movement of southern bean mosaic virus Virology 252 2 1998 376 386
30. P. Skubak, G.N. Murshudov, and N.S. Pannu Direct incorporation of experimental phase information in model refinement Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 Pt. 12 Pt. 1 2004 2196 2201
31. T. Terwilliger SOLVE and RESOLVE: automated structure solution, density modification and model building J. Synchrotron Radiat. 11 Pt. 1 2004 49 52
32. E.C. Wang, S.H. Hung, M. Cahoon, and L. Hedstrom The role of the Cys191-Cys220 disulfide bond in trypsin: new targets for engineering substrate specificity Protein Eng. 10 4 1997 405 411
33. M.P. Weiner, G.L. Costa, W. Schoettlin, J. Cline, E. Mathur, and J.C. Bauer Site-directed mutagenesis of double-stranded DNA by the polymerase chain reaction Gene 151 1-2 1994 119 123
34. J. Wellink, and A. van Kammen Proteases involved in the processing of viral polyproteins. Brief review Arch. Virol. 98 1-2 1988 1 26