Crystal structure of cucumisin, a subtilisin-like endoprotease from cucumis melo L.

Journal of Molecular Biology

Volumn 423, Issue 3, 2012, Pages 386-396

  Murayama, Kazutaka ^a,b   Kato Murayama, Miyuki ^b   Hosaka, Toshiaki ^b   Sotokawauchi, Ami ^c   Yokoyama, Shigeyuki ^b   Arima, Kazunari ^c   Shirouzu, Mikako ^b  

^a TOHOKU UNIVERSITY   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c KAGOSHIMA UNIVERSITY   (Japan)

Author keywords

multidomain protein; plant serine protease; subtilisin like fold; thermostability

Indexed keywords

AMINO ACID; CUCUMISIN; SERINE PROTEINASE; SUBTILASE 3; SUBTILISIN; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; DISULFIDE BOND; MELON; MELTING POINT; NONHUMAN; PRIORITY JOURNAL; THERMOSTABILITY; TOMATO; ULTRACENTRIFUGATION;

CUCUMIS; CUCUMIS MELO; LYCOPERSICON ESCULENTUM;

EID: 84867041792     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.07.013     Document Type: Article

References (31)

1. M. Kaneda, and N. Tominaga Isolation and characterization of a proteinase from the sarcocarp of melon fruit J. Biochem. 78 1975 1287 1296
2. M. Kaneda, H. Ohmine, H. Yonezawa, and N. Tominaga Amino acid sequence around the reactive serine of cucumisin from melon fruit J. Biochem. 95 1984 825 829
3. H. Yonezawa, T. Uchikoba, and M. Kaneda Identification of the reactive histidine of cucumisin, a plant serine protease: modification with peptidyl chloromethyl ketone derivative of peptide substrate J. Biochem. 118 1995 917 920
4. H. Yonezawa, H. Kaizuka, T. Uchikoba, K. Arima, and M. Kaneda Substrate specificity of cucumisin on synthetic peptides Biosci., Biotechnol., Biochem. 64 2000 2104 2108
5. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
6. A. Cedzich, F. Huttenlocher, B.M. Kuhn, J. Pfannstiel, L. Gabler, A. Stintzi, and A. Schaller The protease-associated domain and C-terminal extension are required for zymogen processing, sorting within the secretory pathway, and activity of tomato subtilase 3 (SlSBT3) J. Biol. Chem. 284 2009 14068 14078
7. T. Uchikoba, H. Yonezawa, and M. Kaneda Cleavage specificity of cucumisin, a plant serine protease J. Biochem. 117 1995 1126 1130
8. 2 +-independence and activation by homodimerization of tomato subtilase 3 Proc. Natl Acad. Sci. USA 106 2009 17223 17228
9. H. Yamagata, T. Masuzawa, Y. Nagaoka, T. Ohnishi, and T. Iwasaki Cucumisin, a serine protease from melon fruits, shares structural homology with subtilisin and is generated from a large precursor J. Biol. Chem. 269 1994 32725 32731
10. M. Kaneda, Y. Kamikubo, and N. Tominaga Amino acid sequences of glycopeptides from cucumisin Agric. Biol. Chem. 50 1986 2413 2414
11. L. Hedstrom Serine protease mechanism and specificity Chem. Rev. 102 2002 4501 4524
12. L. Holm, and P. Rosenstrom Dali server: conservation mapping in 3D Nucleic Acids Res. 38 2010 W545 W549
13. K. Bryson, L.J. McGuffin, R.L. Marsden, J.J. Ward, J.S. Sodhi, and D.T. Jones Protein structure prediction servers at University College London Nucleic Acids Res. 33 2005 W36 W38
14. M. Vedadi, F.H. Niesen, A. Allali-Hassani, O.Y. Fedorov, P.J. Finerty Jr., and G.A. Wasney Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination Proc. Natl Acad. Sci. USA 103 2006 15835 15840
15. U.B. Ericsson, B.M. Hallberg, G.T. Detitta, N. Dekker, and P. Nordlund Thermofluor-based high-throughput stability optimization of proteins for structural studies Anal. Biochem. 357 2006 289 298
16. W.F. Li, X.X. Zhou, and P. Lu Structural features of thermozymes Biotechnol. Adv. 23 2005 271 281
17. H. Yamagata, S. Ueno, and T. Iwasaki Isolation and characterization of a possible native cucumisin from developing melon fruits and its limited autolysis to cucumisin Agric. Biol. Chem. 53 1989 1009 1017
18. M. Kaneda, H. Yonezawa, and T. Uchikoba Improved isolation, stability and substrate specificity of cucumisin, a plant serine endopeptidase Biotechnol. Appl. Biochem. 22 1995 215 222
19. C.A. Smith, H.S. Toogood, H.M. Baker, R.M. Daniel, and E.N. Baker Calcium-mediated thermostability in the subtilisin superfamily: the crystal structure of Bacillus Ak.1 protease at 1.8 Å resolution J. Mol. Biol. 294 1999 1027 1040
20. M. Sadeghi, H. Naderi-Manesh, M. Zarrabi, and B. Ranjbar Effective factors in thermostability of thermophilic proteins Biophys. Chem. 119 2006 256 270
21. S. Kumar, C.J. Tsai, and R. Nussinov Factors enhancing protein thermostability Protein Eng. 13 2000 179 191
22. S. Chakravarty, and R. Varadarajan Elucidation of determinants of protein stability through genome sequence analysis FEBS Lett. 470 2000 65 69
23. M.J. Thompson, and D. Eisenberg Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability J. Mol. Biol. 290 1999 595 604
24. R.S. Prajapati, M. Das, S. Sreeramulu, M. Sirajuddin, S. Srinivasan, and V. Krishnamurthy Thermodynamic effects of proline introduction on protein stability Proteins 66 2007 480 491
25. C. Vieille, and G.J. Zeikus Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability Microbiol. Mol. Biol. Rev. 65 2001 1 43
26. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
27. T.C. Terwilliger, and J. Berendzen Automated MAD and MIR structure solution Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 1999 849 861
28. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr., Sect. A: Found. Crystallogr. 47 1991 110 119
29. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 1998 905 921
30. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 1994 760 763
31. DeLano, W. L. (2002). The PyMOL Molecular Graphics System, http://www.pymol.org.