Abstract
Fusarium graminearum (sexual stage: Gibberella zeae) is the causative agent of Fusarium Head Blight (FHB), which is one of the most destructive plant disease of cereals, accounting for high grain yield losses, especially for wheat and maize. Like other fungal pathogens, several extracellular enzymes secreted by G. zeae are known to be involved in host infection. Among these secreted lipases, G. zeae lipase (GZEL), which is encoded by the FGL1 gene, was demonstrated to be crucial to G. zeae pathogenicity. However, the precise mechanism of GZEL remains unclear due to a lack of detailed structural information. In this study, we report the crystal structure of GZEL at the atomic level. The structure of GZEL displays distinct structural differences compared to reported homologues and indicates a unique “double lock” enzymatic mechanism. To gain insight into substrate/inhibitor recognition, we proposed a model of GZEL in complex with substrate and the lipase inhibitor ebelactone B (based on the reported structures of GZEL homologues), which defines possible substrate binding sites within the catalytic cleft and suggests an “anti sn-l” binding mode. These results pave the way to elucidating the mechanism of GZEL and thus provide clues for the design of anti-FHB inhibitors.
Keywords: lipase, Gibberella zeae, crystal structure, mechanism, inhibitor
References
- 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., Terwilliger T.C. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr. 2002;58:1948–1954. doi: 10.1107/S0907444902016657. [DOI] [PubMed] [Google Scholar]
- Bai G., Shaner G. Management and resistance in wheat and barley to fusarium head blight. Annu Rev Phytopathol. 2004;42:135–161. doi: 10.1146/annurev.phyto.42.040803.140340. [DOI] [PubMed] [Google Scholar]
- 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. A serine protease triad forms the catalytic centre of a triacylglycerol lipase. Nature. 1990;343:767–770. doi: 10.1038/343767a0. [DOI] [PubMed] [Google Scholar]
- Brockman H.L., Law J.H., Kézdy F.J. Catalysis by adsorbed enzymes. The hydrolysis of tripropionin by pancreatic lipase adsorbed to siliconized glass beads. J Biol Chem. 1973;248:4965–4970. [PubMed] [Google Scholar]
- 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. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998;54:905–921. doi: 10.1107/S0907444998003254. [DOI] [PubMed] [Google Scholar]
- 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., Thim L. A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex. Nature. 1991;351:491–494. doi: 10.1038/351491a0. [DOI] [PubMed] [Google Scholar]
- Brzozowski A.M., Savage H., Verma C.S., Turkenburg J.P., Lawson D.M., Svendsen A., Patkar S. Structural origins of the interfacial activation in Thermomyces (Humicola) lanuginosa lipase. Biochemistry. 2000;39:15071–15082. doi: 10.1021/bi0013905. [DOI] [PubMed] [Google Scholar]
- Collaborative Computational Project, N., 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr.: 760–763. [DOI] [PubMed]
- Cowtan, K., 1994. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography: 34–38.
- DeLano, W.L. 2002. The PyMOL Molecular Graphics System World Wide Web http://www.pymol.org.
- Derewenda U., Swenson L., Green R., Wei Y., Dodson G.G., Yamaguchi S., Haas M.J., Derewenda Z.S. An unusual buried polar cluster in a family of fungal lipases. Nat Struct Biol. 1994;1:36–47. doi: 10.1038/nsb0194-36. [DOI] [PubMed] [Google Scholar]
- Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. [DOI] [PubMed] [Google Scholar]
- Gouet P., Robert X., Courcelle E. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 2003;31:3320–3323. doi: 10.1093/nar/gkg556. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grochulski P., Bouthillier F., Kazlauskas R.J., Serreqi A.N., Schrag J.D., Ziomek E., Cygler M. Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase. Biochemistry. 1994;33:3494–3500. doi: 10.1021/bi00178a005. [DOI] [PubMed] [Google Scholar]
- Hasan F., Shah A.A., Hameed A. Methods for detection and characterization of lipases: A comprehensive review. Biotechnol Adv. 2009;27:782–798. doi: 10.1016/j.biotechadv.2009.06.001. [DOI] [PubMed] [Google Scholar]
- Hedstrom L. Serine protease mechanism and specificity. Chem Rev. 2002;102:4501–4524. doi: 10.1021/cr000033x. [DOI] [PubMed] [Google Scholar]
- Holm L., Kääriäinen S., Rosenström P., Schenkel A. Searching protein structure databases with DaliLite v.3. Bioinformatics. 2008;24:2780–2781. doi: 10.1093/bioinformatics/btn507. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huey R., Morris G.M., Olson A.J., Goodsell D.S. A semiempirical free energy force field with charge-based desolvation. J Comput Chem. 2007;28:1145–1152. doi: 10.1002/jcc.20634. [DOI] [PubMed] [Google Scholar]
- Jaeger K.E., Reetz M.T. Microbial lipases form versatile tools for biotechnology. Trends Biotechnol. 1998;16:396–403. doi: 10.1016/S0167-7799(98)01195-0. [DOI] [PubMed] [Google Scholar]
- Jones T.A., Zou J.Y., 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. 1991;47:110–119. doi: 10.1107/S0108767390010224. [DOI] [PubMed] [Google Scholar]
- Kohno M., Funatsu J., Mikami B., Kugimiya W., Matsuo T., Morita Y. The crystal structure of lipase II from Rhizopus niveus at 2.2 A resolution. J Biochem. 1996;120:505–510. doi: 10.1093/oxfordjournals.jbchem.a021442. [DOI] [PubMed] [Google Scholar]
- Laskowski R., MacArthur M., Moss D., Thornton J. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst. 1993;26:283–291. doi: 10.1107/S0021889892009944. [DOI] [Google Scholar]
- Matthews B.W. Solvent content of protein crystals. J Mol Biol. 1968;33:491–497. doi: 10.1016/0022-2836(68)90205-2. [DOI] [PubMed] [Google Scholar]
- McAuley K.E., Svendsen A., Patkar S.A., Wilson K.S. Structure of a feruloyl esterase from Aspergillus niger. Acta Crystallogr D Biol Crystallogr. 2004;60:878–887. doi: 10.1107/S0907444904004937. [DOI] [PubMed] [Google Scholar]
- McCoy A.J., Grosse-Kunstleve R.W., Storoni L.C., Read R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr. 2005;61:458–464. doi: 10.1107/S0907444905001617. [DOI] [PubMed] [Google Scholar]
- 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.
- 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. The alpha/beta hydrolase fold. Protein Eng. 1992;5:197–211. doi: 10.1093/protein/5.3.197. [DOI] [PubMed] [Google Scholar]
- 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. [DOI] [PubMed]
- Sarda L., Desnuelle P. Actions of pancreatic lipase on esters in emulsions. Biochim Biophys Acta. 1958;30:513–521. doi: 10.1016/0006-3002(58)90097-0. [DOI] [PubMed] [Google Scholar]
- Schrag J.D., Li Y.G., Wu S., Cygler M. Ser-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum. Nature. 1991;351:761–764. doi: 10.1038/351761a0. [DOI] [PubMed] [Google Scholar]
- 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. The open conformation of a Pseudomonas lipase. Structure. 1997;5:187–202. doi: 10.1016/S0969-2126(97)00178-0. [DOI] [PubMed] [Google Scholar]
- Sun Y., Li M., Zhang Y., Liu L., Liu Y., Liu Z., Li X., Lou Z. Crystallization and preliminary crystallographic analysis of Gibberella zeae extracellular lipase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;64:813–815. doi: 10.1107/S1744309108019283. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876–4882. doi: 10.1093/nar/25.24.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
- van Tilbeurgh H., Egloff M.-P., Martinez C., Rugani N., Verger R., Cambillau C. Interfacial activation of the lipaseprocolipase complex by mixed micelles revealed by X-ray crystallography. Nature. 1993;362:814–820. doi: 10.1038/362814a0. [DOI] [PubMed] [Google Scholar]
- Voigt C.A., Schäfer W., Salomon S. A secreted lipase of Fusarium graminearum is a virulence factor required for infection of cereals. Plant J. 2005;42:364–375. doi: 10.1111/j.1365-313X.2005.02377.x. [DOI] [PubMed] [Google Scholar]
- Winkler F.K., D’Arcy A., Hunziker W. Structure of human pancreatic lipase. Nature. 1990;343:771–774. doi: 10.1038/343771a0. [DOI] [PubMed] [Google Scholar]
- Yapoudjian S., Ivanova M.G., Brzozowski A.M., Patkar S.A., Vind J., Svendsen A., Verger R. Binding of Thermomyces (Humicola) lanuginosa lipase to the mixed micelles of cis-parinaric acid/NaTDC. Eur J Biochem. 2002;269:1613–1621. doi: 10.1046/j.1432-1327.2002.02786.x. [DOI] [PubMed] [Google Scholar]