Crystal structure of a secreted lipase from Gibberella zeae reveals a novel "double-lock" mechanism

Protein and Cell

Volumn 1, Issue 8, 2010, Pages 760-770

  Lou, Zhiyong ^a   Li, Ming ^b   Sun, Yuna ^c   Liu, Ye ^b   Liu, Zheng ^b   Wu, Wenping ^b   Rao, Zihe ^a,c  

^a TSINGHUA UNIVERSITY   (China)

^b Novozymes (China) Investment Co Ltd   (China)

^c INSTITUTE OF BIOPHYSICS   (China)

Author keywords

Crystal structure; Gibberella zeae; Inhibitor; Lipase; Mechanism

Indexed keywords

EBELACTONE B; ENZYME INHIBITOR; GIBBERELLA ZEAE LIPASE; TRIACYLGLYCEROL LIPASE; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME INHIBITOR COMPLEX; ENZYME INHIBITOR INTERACTION; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; GIBBERELLA; GIBBERELLA ZEAE; HYDROGEN BOND; MOLECULAR DOCKING; NONHUMAN; PRIORITY JOURNAL;

FUSARIUM; GIBBERELLA ZEAE; TRITICUM AESTIVUM; ZEA MAYS;

EID: 79953152809     PISSN: 1674800X     EISSN: 16748018     Source Type: Journal    
DOI: 10.1007/s13238-010-0094-y     Document Type: Article

References (37)

1. Adams, P. D., Grosse-Kunstleve, R. W., Hung, L. W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., and Terwilliger, T. C. (2002). PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58, 1948-1954.
2. Bai, G., and Shaner, G. (2004). Management and resistance in wheat and barley to fusarium head blight. Annu Rev Phytopathol 42, 135-161.
3. Brady, L., Brzozowski, A. M., Derewenda, Z. S., Dodson, E., Dodson, G. G., Tolley, S., Turkenburg, J. P., Christiansen, L., Huge-Jensen, B., Norskov, L., et al. (1990). A serine protease triad forms the catalytic centre of a triacylglycerol lipase. Nature 343, 767-770.
4. Brockman, H. L., Law, J. H., and Kézdy, F. J. (1973). Catalysis by adsorbed enzymes. The hydrolysis of tripropionin by pancreatic lipase adsorbed to siliconized glass beads. J Biol Chem 248, 4965-4970.
5. Brünger, 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. (1998). Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54, 905-921.
6. Brzozowski, A. M., Derewenda, U., Derewenda, Z. S., Dodson, G. G., Lawson, D. M., Turkenburg, J. P., Bjorkling, F., Huge-Jensen, B., Patkar, S. A., and Thim, L. (1991). A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex. Nature 351, 491-494.
7. Brzozowski, A. M., Savage, H., Verma, C. S., Turkenburg, J. P., Lawson, D. M., Svendsen, A., and Patkar, S. (2000). Structural origins of the interfacial activation in Thermomyces (Humicola) lanuginosa lipase. Biochemistry 39, 15071-15082.
8. Collaborative Computational Project, N., 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr.: 760-763.
9. Cowtan, K., 1994. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography: 34-38.
10. DeLano, W. L. 2002. The PyMOL Molecular Graphics System World Wide Web http://www. pymol. org.
11. Derewenda, U., Swenson, L., Green, R., Wei, Y., Dodson, G. G., Yamaguchi, S., Haas, M. J., and Derewenda, Z. S. (1994). An unusual buried polar cluster in a family of fungal lipases. Nat Struct Biol 1, 36-47.
12. Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132.
13. Gouet, P., Robert, X., and Courcelle, E. (2003). ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31, 3320-3323.
14. Grochulski, P., Bouthillier, F., Kazlauskas, R. J., Serreqi, A. N., Schrag, J. D., Ziomek, E., and Cygler, M. (1994). Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase. Biochemistry 33, 3494-3500.
15. Hasan, F., Shah, A. A., and Hameed, A. (2009). Methods for detection and characterization of lipases: A comprehensive review. Biotechnol Adv 27, 782-798.
16. Hedstrom, L. (2002). Serine protease mechanism and specificity. Chem Rev 102, 4501-4524.
17. Holm, L., Kääriäinen, S., Rosenström, P., and Schenkel, A. (2008). Searching protein structure databases with DaliLite v. 3. Bioinformatics 24, 2780-2781.
18. Huey, R., Morris, G. M., Olson, A. J., and Goodsell, D. S. (2007). A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28, 1145-1152.
19. Jaeger, K. E., and Reetz, M. T. (1998). Microbial lipases form versatile tools for biotechnology. Trends Biotechnol 16, 396-403.
20. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47, 110-119.
21. Kohno, M., Funatsu, J., Mikami, B., Kugimiya, W., Matsuo, T., and Morita, Y. (1996). The crystal structure of lipase II from Rhizopus niveus at 2. 2 A resolution. J Biochem 120, 505-510.
22. Laskowski, R., MacArthur, M., Moss, D., and Thornton, J. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291.
23. Matthews, B. W. (1968). Solvent content of protein crystals. J Mol Biol 33, 491-497.
24. McAuley, K. E., Svendsen, A., Patkar, S. A., and Wilson, K. S. (2004). Structure of a feruloyl esterase from Aspergillus niger. Acta Crystallogr D Biol Crystallogr 60, 878-887.
25. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C., and Read, R. J. (2005). Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr 61, 458-464.
26. Nganje, W. E., Johnson, D. D., Wilson, W. W., Leistritz, F. L., Bangsund, D. A., and Tiapo, N. M. 2001. Economic impacts of fusarium head blight in wheat and barley: 1998-2000. In Agribusiness and Applied Economics Report No. 464.
27. Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schrag, J., et al. (1992). The alpha/beta hydrolase fold. Protein Eng 5, 197-211.
28. Otwinowski, Z., and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode, p. 307-326, in: C. W. Carter Jr. and R. M. Sweet, Eds.), Macromolecular Crystallography, part A, Academic Press.
29. Sarda, L., and Desnuelle, P. (1958). Actions of pancreatic lipase on esters in emulsions. Biochim Biophys Acta 30, 513-521.
30. Schrag, J. D., Li, Y. G., Wu, S., and Cygler, M. (1991). Ser-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum. Nature 351, 761-764.
31. Schrag, J. D., Li, Y., Cygler, M., Lang, D., Burgdorf, T., Hecht, H.-J., Schmid, R., Schomburg, D., Rydel, T. J., Oliver, J. D., et al. (1997). The open conformation of a Pseudomonas lipase. Structure 5, 187-202.
32. Sun, Y., Li, M., Zhang, Y., Liu, L., Liu, Y., Liu, Z., Li, X., and Lou, Z. (2008). Crystallization and preliminary crystallographic analysis of Gibberella zeae extracellular lipase. Acta Crystallogr Sect F Struct Biol Cryst Commun 64, 813-815.
33. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
34. van Tilbeurgh, H., Egloff, M.-P., Martinez, C., Rugani, N., Verger, R., and Cambillau, C. (1993). Interfacial activation of the lipaseprocolipase complex by mixed micelles revealed by X-ray crystallography. Nature 362, 814-820.
35. Voigt, C. A., Schäfer, W., and Salomon, S. (2005). A secreted lipase of Fusarium graminearum is a virulence factor required for infection of cereals. Plant J 42, 364-375.
36. Winkler, F. K., D'Arcy, A., and Hunziker, W. (1990). Structure of human pancreatic lipase. Nature 343, 771-774.
37. Yapoudjian, S., Ivanova, M. G., Brzozowski, A. M., Patkar, S. A., Vind, J., Svendsen, A., and Verger, R. (2002). Binding of Thermomyces (Humicola) lanuginosa lipase to the mixed micelles of cis-parinaric acid/NaTDC. Eur J Biochem 269, 1613-1621.