Lipases: Molecular structure and function

Industrial Enzymes: Structure, Function and Applications

Volumn , Issue , 2007, Pages 263-281

  Lotti, Marina ^a   Alberghina, Lilia ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84892335674     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/1-4020-5377-0_16     Document Type: Chapter

References (95)

1. Acharya, P., Rajakumara, E., Sankaranarayanan, R. and Rao, N.M. (2004) Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. J. Mol. Biol. 341(5), 1271-1281.
2. Arnold, F.H. and Georgiou, G. (2003) Directed Evolution vols 230 and 231. Humana Press, Totowa, New Jersey. Bornscheuer, U.T. (ed.) Enzymes in lipid modification. Wiley VCH, 2000.
3. Bornscheuer, U.T., Bessler, C., Srinivas, R. and Krishna, S.H. (2002) Optimizing lipases and related enzymes for efficient application. Trends Biotechnol. 20(10), 433-437.
4. Brady, L., Brzozowski, A.M., Derewenda, Z.S., Dodson, E., Dodson, G., Tolley, S., Turkenburg, J.P., Christiansen, L., Huge-Jensen, B., Norskov, L., Thim, L. and Menge, U. (1990) A serine protease triad forms the catalytic center of a triacylglycerol lipase. Nature 343, 767-770.
5. Brocca, S., Persson, M., Wehtje, E., Adlercreutz, P., Alberghina, L. and Lotti, M. (2000) Mutants provide evidence of the importance of glycosydic chains in the activation of lipase 1 from Candida rugosa. Prot. Sci. 9, 985-990.
6. Brocca, S., Secundo, F., Ossola, M., Alberghina, L., Carrea, G. and Lotti, M. (2003) Sequence of the lid affects activity and specificity of Candida rugosa lipase isoenzymes. Prot. Sci. 12, 2312-2319.
7. 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.
8. 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. J. Biochem. 39, 15071-15082.
9. Carrière, F., Withers-Martinez, C., van Tilbeurgh, H., Roussel, A., Cambillau, C. and Verger, R. (1998) Structural basis for the substrate selectivity of pancreatic lipases and some related proteins. Biochim. Biophys. Acta 1376, 417-432.
10. Cernia, E.and Palocci, C. (1997) Lipases in supercritical fluids. Methods Enzymol. 286, 495-508.
11. Demirhian, D.C., Moris-Varas, F. and Cassidy, C.S. (2001) Enzymes from extremophiles. Curr. Opinion Chem. Biol. 5, 144-151.
12. 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.
13. Drauz, K. and Waldmann, H. (1995) Enzyme Catalysis in Organic Synthesis. Wiley-VCH Verlag, GmbH, Weinheim.
14. Eggert, T., Leggewie, C., Puls, M., Streit, W., van Pouderoyen, G., Dijkstra, B.W. and Jaeger, K.-E. (2004) Novel Biocatalysts by identification and design. Biocat. Biotrans. 22, 139-144.
15. Eggert, T., Funke, S.A., Rao, N.M., Acharya, P., Krumm, H., Reetz, M.T. and Jaeger, K.-E. (2005) Multiplex-PCR-based recombination as a novel high-fidelity method for directed evolution ChemBiochem 6(6), 1062-1067.
16. Fickers, P., Fudalej, F., Le Dall, M.T., Casaregola, S., Gaillardin, C., Thonart, P. and Nicaud, J.M. (2005) Identification and characterization of LIP7 and LIP8 genes encoding two extracellular triacylglycerol lipases in the yeast Yarrowia lipolytica. Fungal genetics and biology 42(3), 264-274.
17. Fisher, M. and Pleiss, J. (2003) The lipase engineering database: a navigation and analysis tool for protein families. Nucl. Acid Res. 31(1), 319-321.
18. Fujii, R., Nakagawa, Y., Hiratake, J., Sogabe, A. and Sakata, K. (2005) Directed evolution of Pseudomonas aeruginosa lipase for improved amide-hydrolyzing activity. Prot. Eng. Des. Sel. 18(2), 93-101.
19. Funke, S.A., Eipper, A., Reetz, M.T., Otte, N., Thiel, W., Van Pouderoyen, G., Dijkstra, B.W., Jaeger, K.-E. and Eggert, T. (2003) Directed evolution of an enantioselective Bacillus subtilis lipase. Biocat. Biotransf. 21(2), 67-73.
20. Ghosh, D., Wawrzak, Z., Pletnev, V.Z., Li, N.Y., Kaiser, R., Pangborn, W., Jornvall, H., Erman, M. and Duax, W.L. (1995) Structure of uncomplexed and linoleate-bound Candida cylindracea cholesterol esterase. Structure 3, 279-288.
21. Grochulski, P., Li, Y., Schrag, J.D., Bouthillier, F., Smith, P., Harrison, D., Rubin, B. and Cygler, M. (1993) Insights into interfacial activation from an open structure of Candida rugosa lipase. J. Biol. Chem. 268, 12843-12847.
22. Grochulski, P., Li, Y., Schrag, J.D. and Cygler, M. (1994) Two conformational states of Candida rugosa lipase. Prot. Sci. 3, 82-91.
23. Gupta, R., Gupta, N. and Rathi, P. (2004) Bacterial lipases: An overview of production, purification and biochemical properties. Appl. Microbiol. Biotechnol. 64, 763-781.
24. Han, S.J., Chung, J.H., Cheong, C.S., Chung, I.Y. and Han, Y.S. (2004) Enhancement of lipase activity from Acinetobacter species SY-01 by random mutagenesis and the role of lipase-specific chaperone. Enz. Microb. Technol. 35(5), 377-384.
25. Henne, A., Schmitz, R.A., Bomeke, M., Gottschalk, G. and Daniel, R. (2000) Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl. Environ. Microbiol. 66, 3113-3116.
26. Hube, B., Stehr, F., Bossenz, M., Mazur, A., Kretschmar, M. and Schafer, W. (2000) Secreted lipases of Candida albicans: Cloning, characterization and expression analysis of a new gene family with at least ten members. Arch. Microbiol. 174(5), 362-374.
27. Hulo, N., Sigrist, C.J.A., Le Saux, V., Langendijk-Genevaux, P.S., Bordoli, L., Gattike, A., De Castro, E., Bucher, P. and Bairoch, A. (2004) Recent improvements to the PROSITE database. Nucl. Acids. Res. 32, D134-D137.
28. Jaeger, K.-E. and Eggert, T. (2002) Lipases for biotechnology. Curr. Opin. Biotechnol. 13, 390-397.
29. Jaeger, K.-E. and Eggert, T. (2004) Enantioselective biocatalysis optimized by directed evolution. Curr. Opin. Biotechnol. 15, 305-313.
30. Jaeger, K.-E., Dijkstra, B.W. and Reetz, M.T. (1999) Bacterial biocatalysts: Molecular biology, three dimensional structures, and biotechnological applications of lipases. Ann. Rev. Microbiol. 53, 315-351.
31. Jenkins-Kruchten, A.E., Bennaars-Eiden, A., Rossi, J.R., Shen, W-J., Kraemer, F.B. and Bernlohr, D.A. (2003) Fatty acid-binding protein-Hormone- sensitive lipase interaction. Fatty acid dependence of binding. J. Biol. Chem. 278, 47636-47643.
32. Kauffmann, I. and Schmidt-Dannert, C. (2001) Conversion of Bacillus thermocatenulatus lipase into an efficient phospholipase with increased activity towards long-chain fatty acyl substrates by directed evolution and rational design. Prot. Eng. 14, 919-928.
33. Kazlauskas, R.J. (2005) Enhancing catalytic promiscuity for biocatalysis. Curr. Opinion Chem. Biol. 9, 195-201.
34. Kim, H.K., Jung, Y-J., Choi, W-C., Ryu, H.S., Oh, T-K. and Lee, J-K. (2004) Sequence-based approach to finding functional lpases from microbial genome databases. FEMS Microbiol. Letters 235, 349-355.
35. Kirk, O., Borchert, T.V. and Fuglsang, C.C. (2002) Industrial enzyme applications. Curr. Opin. Biotechnol. 13, 345-351.
36. Klein, R.R., King, G., Moreau, R.A. and Haas, M.J. (1997) Altered acyl chain length specificity of Rhizopus delemar lipase through mutagenesis and molecular modeling. Lipids 32(2), 123-130.
37. Koga, Y., Kato, K., Nakano, H., Yamane, T. (2003) Inverting enantioselectivity of Burkholderia cepacia KWI-56 lipase by combinatorial mutation and high-throughput screening using single-molecule PCR and in vitro expression. J. Mol. Biol. 331(3), 585-592.
38. 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 angstrom resolution. J. Biochem. 120, 505-510.
39. Kovac, A., Scheib, H., Pleiss, J., Schmid, R.D. and Paltauf, F. (2000) Molecular basis of lipase stereoselectivity. Eur. J. Lipid Sci. Technol. 2000: 61-77.
40. Lang, D.A., Mannesse, M.L.M., de Haas, G.H., Verheij, H.M. and Dijkstra B.W. (1998) Structural basis of the chiral selectivity of Pseudomonas cepacia lipase. Eur. J. Biochem. 254, 333-340.
41. Le, G.T., Abbenante, G., Becker, B., Grathwohl, M., Halliday, J., Tometzki, G., Zuegg, J. and Meutermans, W. (2003) Molecular diversity through sugar scaffolds. Drug Discovery today: 8, 701 and refs. cited therein.
42. Lee, G.C., Tang, S.J., Sun, K.H. and Shaw, J.F. (1999) Analysis of the gene family encoding lipases in Candida rugosa by competitive reverse transcription PCR. Appl. Environ. Microbiol. 65, 3888-3895.
43. Liebton, K., Zonta, A., Schimossek, K., Nardini, M., Lang, D., Dijkstra, B.W., Reetz, M.T. and Jaeger, K-E. (2000) Directed evolution of an enantioselctive lipase. Chem. Biol. 2000(7), 709-718.
44. Lombardo, D., Chapus, C., Bourne, Y. and Cambillau, C. (1989) Crystallization and preliminary X-ray study of horse pancreatic lipase. J. Mol. Biol. 205, 259-261.
45. Lopez, N., Pernas, M.A., Pastrana, L.M., Sanchez, A., Valero, F. and Rua, M.L. (2004) Reactivity of pure Candida rugosa lipase isoenzymes (Lip1, Lip2 and Lip3) in aqueous and organic media. Influence of the isoenzymatic profile on the lipase performances in organic media. Biotechnol. Prog. 20, 65-73.
46. Lotti, M., Grandori, R., Fusetti, F., Longhi, S., Brocca, S., Tramontano, A. and Alberghina, L. (1993) Cloning and analysis of Candida cylindracea lipase sequences. Gene 124, 45-55.
47. Lotti, M., Monticelli, S., Montesinos, J.L., Brocca, S., Valero, F. and Lafuente, J. (1998) Physiological control on the expression and secretion of Candida rugosa lipase. Chem. Phys. of Lipids 93(1-2) 143-148.
48. Magnusson, A.O., Roticci-Mulder, J.C., Santagostino, A. and Hult, K. (2005) Creating space for large secondary alcohols by rational redesign of Candida antarctica lipase B. Chem. Bio. Chem. 6, 1051-1056.
49. Mancheno, J.M., Pernas, M.A., Martinez, M.J., Ochoa, B., Rua, M.L. and Hermoso, J.A. (2003) Structural insights into the lipase/esterase behavior in the Candida rugosa lipases family: Crystal structure of the lipase 2 isoenzyme at 1.97 angstrom resolution. J. Mol. Biol. 332, 1059-1069.
50. Martinez, C., De Geus, P., Lauwereys, M., Matthyssens, G. and Cambillau, C. (1992) Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent. Nature 356, 615-618.
51. Miller, G.C., Long, C.U.J., Bojilova, E.D., Marchandier, D., Badellino, K.O., Blanchard, N., Fuki, I.V., Glick, J.M. and Rader, D.J. (2004) Role of N-linked glycosylation in the secretion and activity of endothelial lipase. J. Lipid Res. 45(11), 2080-2087.
52. Mukherijee, K.D. and Hills, M.J. (1994) Lipases from plants. In: Woolley P., Petersen S.B. eds Lipases: their structure, biochemistry and application. Cambridge University Press, pp. 49-75.
53. Müller, G. and Petry, S. eds. Lipases and phospholipases in drug development: from biochemistry to molecular pharmacology, Wiley VCH, 2004.
54. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: A structural classification of proteins databases for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540. http://scop.mrc-lmb.cam. ac.uk/scop/
55. Nardini, M., Lang, D.A., Liebeton, K., Jaeger, K.E. and Dijkstra, B.M. (2000) Crystal structure of Pseudomonas aeruginosa lipase in the open conformation - The prototype for family I.1 of bacterial lipases. J. Biol. Chem. 275(40), 31219-31225.
56. Noble, M.E., Cleasby, A., Johnson, L.N., Egmond, M.R. and Frenken, L.G. (1993) The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate. FEBS Lett. 331, 123-128.
57. Ollis, D.L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S.M., Harel, M., Remington, S.J., Silman, I., Schrag, J., Sussman, J.L., Verschueren, K.H.G. and Goldman, A. (1992) The alpha/betahydrolase fold. Prot. Eng. 5, 197-211.
58. Park, S. and Kazlauskas, R.J. (2003) Biocatalysis in ionic liquids-advantages beyond green technology. Curr. Opin. Biotechnol. 14, 432-437.
59. Peters, G.H., Svendsen, A., Langberg, H., Vind, J., Patkar, S.A. and Kinnunen, P.K.J. (2002) Glycosylation of Thermomyces lanuginosa lipase enhances surface binding towards phospholipids, but does not significantly influence the catalytic activity. Colloids and Surface B-Biointerfaces 26(1-2) 125-134.
60. Pleiss, J., Fisher, M. and Schmid, R.D. (1998) Anatomy of lipase binding sites : tThe scissile fatty acid binding sites. Chem. Phys. Lipids 93, 67-80.
61. Qian, Z., and Lutz, S. (2005). Improving the catalytic activity of Candida antarctica lipase B by circular permutation. J. Am. Chem. Soc. 127 (39), 13466-13467.
62. Ransac, S., Rogalska, E., Gargouri, Y., Deveer, A. M., Paltauf, F., de Haas, G. H. and Verger, R. (1990). Stereoselectivity of lipases. I. Hydrolysis of enantiomeric glyceride analogues by gastric and pancreatic lipases, a kinetic study using the monomolecular film technique. J. Biol. Chem. 265, 20263-20270.
63. Reetz, M.T., Bocola, M., Carballeira, J.D., Zha, D.X. and Vogel, A. (2005). Expanding the range of substrate acceptance of enzymes: Combinatorial active-site saturation test. Angew. Chem. Int. Ed. 44 (27), 4192-4196.
64. Reyes-Duarte, D., Polaina, J., Lopez-Cortés, N., Alcade, M., Plou, F.J., Elborough, K., Ballesteros, A., Timmis, K.N., Golyshin, P.N. and Ferrer, M. (2005) Conversion of a carboxylesterase into a triacylglycerol lipase by a random mutation. Angew. Chem. Int. Ed. 44, 7553-7557.
65. Roticci, D., Roticci-Mulder, J.C., Denman, S., Norin, T., and Hult, K. (2001). Improved enantioselectivity of a lipase by rational protein engineering. Chem Biol Chem 2, 766-770.
66. Roussel, A., Yang, Y.Q., Ferrato, F., Verger, R., Cambillau, C. and Lowe, M. (1998). Structure and activity of rat pancreatic lipase-related protein 2. J. Biol. Chem. 273, 32121-32128.
67. Roussel, A., Canaan, Egloff, M.P., Riviere, M., Dupuis, L., Verger, R., and Cambillau, C. (1999). Crystal structure of human gastric lipase and model of lysosomal acid lipase, two lipolytic enzymes of medical interest. J. Biol. Chem. 274, 16995-17002.
68. Roussel, A., Miled, N., Berti-Dupuis, L., Riviere, M., Spinelli, S., Berna, P., Gruber, V., Verger, R. and Cambillau, C. (2002). Crystal structure of the open form of dog gastric lipase in complex with a phosphonate inhibitor. J. Biol. Chem. 277, 2266-2274.
69. Santarossa, G., Gatti Lafranconi, P., Alquati, C., De Gioia, L., Alberghina, L., Fantucci, P. and Lotti, M (2005). Mutations in the "lid" regions affect chain length specificity and thermostability of a Pseudomonas fragi lipase. FEBS Letters 579, 2383-2386.
70. Sarda, L. and Desnuelle, P. (1958). Action de la lipase pancréatique sur les esters en émulsion. Biochim. Biophys. Acta 30, 513-521.
71. Schmid, R. D. and Verger, R. (1998). Lipases: interfacial enzymes with attractive applications. Angew. Chem. Int. Ed. 37, 1608-1633.
72. Schmidt, A., Dordick, J.S., Hauer, B., Kiener, A., Wubbolts, M. and Witholt, B. (2001). Industrial biocatalysts today and tomorrow. Nature 2001 409, 258-268.
73. Schmitt, J., Brocca, S., Schmid, R.D. and Pleiss, J. (2002). Blocking the tunnel: engineering of Candida rugosa lipase mutants with short chain length specificity. Prot. Eng. 15, 595-601.
74. Scharg, J.D.and Cygler, M. (1993). 1.8-Angstrom refined structure of the lipase from Geotrichum candidum. J. Mol. Biol. 230, 575-591.
75. Scharg, J.D., Li, Y., Cygler, M., Lang, D., Burgdorf, T., Hecht, H.J., Schmid, R., Schomburg, D., Rydel, T.J., Oliver, J.D., Strickland, L.C., Dunaway, C.M., Larson, S.B., Day, J. and Mcpherson, A. (1997). The open conformation of a Pseudomonas lipase. Structure 5(2): 187-202.
76. Shibamoto, H., Matsumoto, T., Fukuda, H., and Kondo, A. (2004) Molecular engineering of Rhizopus oryzae lipase using a combinatorial protein library constructed on the yeast cell surface. J. Mol. Cat. B: Enzymatic (4-6) 235-239.
77. Shibatani, T., Nakamichi, K. and Matsumae, H. (1990). European Patent Application EP 362556.
78. Suen, W.C., Zhang, N.Y., Xiao, L., Madison, V. and Zaks, A. (2004) Improved activity and thermostability of Candida antarctica lipase B by DNA family shuffling. Prot. Eng. Des. 17(2), 133-140.
79. Svendsen, A. (2000). Lipase protein engineering. Biochim. Biophys. Acta 1543(2), 223-238.
80. Terzyan, S., Wang, C.S., Downs, D., Hunter, B.and Zhang, X.C. (2000). Crystal structure of the catalytic domain of human bile salt activated lipase. Prot. Sci. 9, 1783-1790.
81. Tyndall, J.D.A., Sinchaikul, S., Fothergill-Gilmore, L.A., Taylor, P., and Walkinshaw, M.D. (2002). Crystal structure of a thermostable lipase from Bacillus stearothermophilus P1. J. Mol. Biol. 323, 859-869.
82. Uppenberg, J., Patkar, S., Bergfors, T. and Jones, T.A. (1994). Crystallization and preliminary X-ray studies of lipase B from Candida antarctica. J. Mol. Biol. 235, 790-792.
83. van Kampen, M.D. and Egmond, M.R. (2000). Directed evolution: from a staphylococcal lipase to a phospholipase. Eur. J. Lipid Sci. Technol. 102, 717-726.
84. van Pouderoyen, G., Eggert, T., Jaeger, K.-E. and Dijkstra, B.W. (2001). The crystal structure ofBacillus subtilis lipase: a minimal alpha/beta hydrolase fold enzyme. J. Mol. Biol. 309(1), 215-226.
85. van Tilbeurgh, H., Sarda, L., Verger, R. and Cambillau, C. (1992). Structure of the pancreatic lipase- procolipase complex Nature 359, 159-162.
86. Verger, R. (1997). "Interfacial activation" of lipases: facts and artifacts. Trends Biotechnol. 15, 32-38.
87. Villeneuve, P., Muderhwa, J.M., Graille, J. and Haas, M.J. (2000). Customizing lipases for biocatalysis: a survey of chemical, physical and molecular biological approaches. J. Mol. Catal. B: Enzymatic 9, 113-148.
88. Voget, S., Leggewie, C., Uesbeck, A., Raasch, C., Jaeger, K.-E. and Streit, W.R. (2003). Prospecting for novel biocatalysts in a soil metagenome. Appl. Environ. Microbiol. 69, 6235-6242.
89. Wei, Y., Swenson, L., Castro, C., Derewenda, U., Minor,W., Arai, H., Aoki, J., Inoue, K., Servin- Gonzalez, L. and Derewenda, Z.S. (1998). Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution. Structure 6, 511-519.
90. Wicker-Planquart, C., Canaan, S., Rivière, M. and Depuis, L. (1999). Site-directed removal of N-glycosylation sites in human gastric lipase. Eur. J. Biochem. 262, 644-651.
91. Winkler, FK, D'Arcy, A. and Hunziker W. (1990). Structure of human pancreatic lipase. Nature 343, 771-774.
92. Yeaman, S. J. (2004). Hormone-sensitive lipase - new roles for an old enzyme. Biochem. J. 379, 11-22.
93. Zschenker, O., Bahr, C., Hess, U.F. and Ameis, D. (2005). Systematic mutagenesis of potential glycosylation sites of lysosomal acid lipase. J. Biochem. 137(3), 387-394.
94. Zaks, A., and Klibanow, A. M. (1984). Enzymatic catalysis in organic media at 100 °C. Science 224, 1249-1251.
95. Zha, D.X., Wilensek, S., Hermes, M., Jaeger, K.-E. and Reetz M.T. (2001). Complete reversal of enantioselectivity of an enzyme-catalyzed reaction by directed evolution. Chem. Commun. 2001, 2664-2665.