Crystal Structure of a Novel Viral Protease with a Serine/Lysine Catalytic Dyad Mechanism

Journal of Molecular Biology

Volumn 358, Issue 5, 2006, Pages 1378-1389

  Feldman, Anat R ^a   Lee, Jaeyong ^a   Delmas, Bernard ^b   Paetzel, Mark ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b INRA Institut National de la Recherche Agronomique   (France)

Author keywords

birnavirus; lysine general base; polyprotein; serine lysine catalytic dyad; viral protease

Indexed keywords

ENDOPEPTIDASE LA; LEXA PROTEIN; LYSINE; PROTEINASE; SERINE; VIRUS ENZYME; RECOMBINANT PROTEIN; SERINE PROTEINASE; VP4 PROTEASE, BIRNAVIRUS;

ARTICLE; BINDING SITE; BIRNAVIRIDAE; BLOTCHED SNAKEHEAD VIRUS; CATALYSIS; CRYSTAL STRUCTURE; ENZYME SUBSTRATE; NONHUMAN; PRIORITY JOURNAL; AMINO ACID SEQUENCE; AQUABIRNAVIRUS; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

BIRNAVIRIDAE; BLOTCHED SNAKEHEAD VIRUS; INFECTIOUS BURSAL DISEASE VIRUS; INFECTIOUS PANCREATIC NECROSIS VIRUS; MIRIDAE;

AMINO ACID SEQUENCE; AQUABIRNAVIRUS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; LYSINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SERINE; SERINE ENDOPEPTIDASES;

EID: 33745041491     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.02.045     Document Type: Article

References (43)

1. Babe L.M., and Craik C.S. Viral proteases: evolution of diverse structural motifs to optimize function. Cell 91 (1997) 427-430
2. Tong L. Viral proteases. Chem. Rev. 102 (2002) 4609-4626
3. Dobos P., Hill B.J., Hallett R., Kells D.T., Becht H., and Teninges D. Biophysical and biochemical characterization of five animal viruses with bisegmented double-stranded RNA genomes. J. Virol. 32 (1979) 593-605
4. Petit S., Lejal N., Huet J.C., and Delmas B. Active residues and viral substrate cleavage sites of the protease of the birnavirus infectious pancreatic necrosis virus. J. Virol. 74 (2000) 2057-2066
5. Coulibaly F., Chevalier C., Gutsche I., Pous J., Navaza J., Bressanelli S., et al. The birnavirus crystal structure reveals structural relationships among icosahedral viruses. Cell 120 (2005) 761-772
6. John K.R., and Richards R.H. Characteristics of a new birnavirus associated with a warm-water fish cell line. J. Gen. Virol. 80 (1999) 2061-2065
7. Da Costa B., Soignier S., Chevalier C., Henry C., Thory C., Huet J.C., and Delmas B. Blotched snakehead virus is a new aquatic birnavirus that is slightly more related to avibirnavirus than to aquabirnavirus. J. Virol. 77 (2003) 719-725
8. Lejal N., Da Costa B., Huet J.C., and Delmas B. Role of Ser-652 and Lys-692 in the protease activity of infectious bursal disease virus VP4 and identification of its substrate cleavage sites. J. Gen. Virol. 81 (2000) 983-992
9. Birghan C., Mundt E., and Gorbalenya A.E. A non-canonical lon proteinase lacking the ATPase domain employs the Ser-Lys catalytic dyad to exercise broad control over the life cycle of a double-stranded RNA virus. EMBO J. 19 (2000) 114-123
10. Rawlings N.D., and Barrett A.J. MEROPS: the peptidase database. Nucl. Acids Res. 27 (1999) 325-331
11. Paetzel M., and Dalbey R.E. Catalytic hydroxyl/amine dyads within serine proteases. Trends Biochem. Sci. 22 (1997) 28-31
12. Paetzel M., and Strynadka N.C. Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism. Protein Sci. 8 (1999) 2533-2536
13. Paetzel M., Dalbey R.E., and Strynadka N.C. Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor. Nature 396 (1998) 186-190
14. Luo Y., Pfuetzner R.A., Mosimann S., Paetzel M., Frey E.A., Cherney M., et al. Crystal structure of LexA: a conformational switch for regulation of self-cleavage. Cell 106 (2001) 1-10
15. Bell C.E., Frescura P., Hochschild A., and Lewis M. Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding. Cell 101 (2000) 801-811
16. Peat T.S., Frank E.G., McDonald J.P., Levine A.S., Woodgate R., and Hendrickson W.A. Structure of the UmuD′ protein and its regulation in response to DNA damage. Nature 380 (1996) 727-730
17. Botos I., Melnikov E.E., Cherry S., Tropea J.E., Khalatova A.G., Rasulova F., et al. The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J. Biol. Chem. 279 (2004) 8140-8148
18. Burgi H.B., Dunitz J.D., and Shefter E. Geometric reaction coordinates. II. Nucleophilic addition to a carbonyl group. J. Am. Chem. Soc. 95 (1973) 5065-5067
19. Schechter I., and Berger A. On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun. 27 (1967) 157-162
20. Paetzel M., Dalbey R.E., and Strynadka N.C. Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism. J. Biol. Chem. 277 (2002) 9512-9519
21. Paetzel M., Goodall J.J., Kania M., Dalbey R.E., and Page M.G. Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor. J. Biol. Chem. 279 (2004) 30781-33090
22. Im Y.J., Na Y., Kang G.B., Rho S.H., Kim M.K., Lee J.H., et al. The active site of a lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic Dyad of Lon proteases. J. Biol. Chem. 279 (2004) 53451-53457
23. Botos I., Melnikov E.E., Cherry S., Kozlov S., Makhovskaya O.V., Tropea J.E., et al. Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases. J. Mol. Biol. 351 (2005) 144-157
24. Holm L., and Sander C. Touring protein fold space with Dali/FSSP. Nucl. Acids Res. 26 (1998) 316-319
25. Ponstingl H., Henrick K., and Thornton J.M. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins: Struct. Funct. Genet. 41 (2000) 47-57
26. Otwinowski Z. Denzo. In: Sawyer L., Isaacs N., and Baily S. (Eds). Denzo (1993), SERC Daresbury Laboratory, Warrington, UK 56-62
27. Vonrhein C., Blanc E., Roversi P., and Bricogne G. Automated structure solution with autoSHARP. In: Doublie S. (Ed). Crystallographic Methods (2005), Humana Press, Totowa, NJ
28. Abrahams J.P., and Leslie A.G. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallog. sect. D 52 (1996) 30-42
29. Morris R.J., Perrakis A., and Lamzin V.S. ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol. 374 (2003) 229-244
30. McRee D.E. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
31. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
32. Winn M.D., Isupov M.N., and Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallog. sect. D 57 (2001) 122-133
33. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
34. Hutchinson E.G., and Thornton J.M. PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci. 5 (1996) 212-220
35. Hutchinson E.G., and Thornton J.M. HERA-a program to draw schematic diagrams of protein secondary structures. Proteins: Struct. Funct. Genet. 8 (1990) 203-212
36. Diederichs K. Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm. Proteins: Struct. Funct. Genet. 23 (1995) 187-195
37. Maiti R., Van Domselaar G.H., Zhang H., and Wishart D.S. SuperPose: a simple server for sophisticated structural superposition. Nucl. Acids Res. 32 (2004) W590-W594
38. C.C.P. no. 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
39. Liang J., Edelsbrunner H., and Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7 (1998) 1884-1897
40. Tsodikov O.V., Record Jr. M.T., and Sergeev Y.V. Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem. 23 (2002) 600-609
41. Kraulis P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog 24 (1991) 946-950
42. Meritt E.A., and Bacon D.J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
43. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28 (2000) 235-242