Open and closed states of Candida Antarctica lipase B: Protonation and the mechanism of interfacial activation

Journal of Lipid Research

Volumn 56, Issue 12, 2015, Pages 2348-2358

  Stauch, Benjamin ^a   Fisher, Stuart J ^b   Cianci, Michele ^c  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b DIAMOND LIGHT SOURCE LTD   (United Kingdom)

^c DESY   (Germany)

Author keywords

Enzymology enzyme regulation; Fatty acid metabolism; Lipids chemistry; X ray crystallography

Indexed keywords

LIPASE B; FUNGAL PROTEIN; LIPASE B, CANDIDA ANTARCTICA; TRIACYLGLYCEROL LIPASE;

ARTICLE; CANDIDA ANTARCTICA; CRYSTAL STRUCTURE; CRYSTALLIZATION; DERIVATIZATION; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME REGULATION; INTERFACIAL ACTIVATION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTON TRANSPORT; STRUCTURE ANALYSIS; X RAY DIFFRACTION; CHEMISTRY; METABOLISM; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; FUNGAL PROTEINS; LIPASE; PROTEIN CONFORMATION;

EID: 84948756336     PISSN: 00222275     EISSN: 15397262     Source Type: Journal    
DOI: 10.1194/jlr.M063388     Document Type: Article

References (42)

1. Wong, H. 2002. The lipase gene family. J. Lipid Res. 43 : 993 - 999.
2. Lotti, M., and L. Alberghina. 2007. Lipases: molecular structure and function. In Industrial Enzymes: Structure, Function and Applications. J. Polaina and A. P. MacCabe, editors. Springer, Dordrecht, The Netherlands. 263-281.
3. Sarda, L., and P. Desnuelle. 1958. Actions of pancreatic lipase on esters in emulsions. Biochim. Biophys. Acta. 30 : 513 - 521.
4. Winkler, F. K., A. D'Arcy, and W. Hunziker. 1990. Structure of human pancreatic lipase. Nature. 343 : 771 - 774.
5. van Tilbeurgh, H., L. Sarda, R. Verger, and C. Cambillau. 1992. Structure of the pancreatic lipase-procolipase complex. Nature. 359 : 159 - 162.
6. Egloff, M-P., F. Marguet, G. Buono, R. Verger, C. Cambillau, and H. v. Tilbeurgh. 1995. The 2.46 A resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate. Biochemistry. 34 : 2751 - 2762.
7. Schrag, J. D., and M. Cygler. 1993. 1.8 Å refi ned structure of the lipase from Geotrichum candium. J. Mol. Biol. 230 : 575 - 591.
8. Noble, M. E. M., A. Cleasby, L. N. Johnson, M. R. Egmondb, and L. G. J. Frenkenb. 1993. The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate. FEBS Lett. 331 : 123 - 128.
9. Verger, R. 1997. "Interfacial activation" of lipases: facts and artifacts. Trends Biotechnol. 15 : 32 - 38.
10. Ericsson, D. J., A. Kasrayan, P. Johansson, T. Bergfors, A. G. Sandstrom, J. E. Backvall, and S. L. Mowbray. 2008. X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation. J. Mol. Biol. 376 : 109 - 119.
11. Roussel, A., S. Amara, A. Nyyssola, E. Mateos-Diaz, S. Blangy, H. Kontkanen, A. Westerholm-Parvinen, F. Carriere, and C. Cambillau. 2014. A cutinase from Trichoderma reesei with a lidcovered active site and kinetic properties of true lipases. J. Mol. Biol. 426 : 3757 - 3772.
12. Anderson, E. M., K. M. Larsson, and O. Kirk. 1998. One biocatalyst- many applications: The use of Candida antarctica B-lipase in organic synthesis. Biocatal. Biotransformation. 16 : 181 - 204.
13. Rotticci, D., J. C. Rotticci-Mulder, S. Denman, T. r. Norin, and K. Hult. 2001. Improved enantioselectivity of a lipase by rational protein engineering. ChemBioChem. 2 : 766 - 770.
14. Uppenberg, J., M. T. Hansen, S. Patkar, and T. A. Jones. 1994. The sequence, crystal structure determination and refi nement of two crystal forms of lipase B from Candida antarctica. Structure. 2 : 293 - 308.
15. Uppenberg, J., N. Ohmer, M. Norin, K. Hult, G. J. Kleywegt, S. Patkar, V. Waagen, T. Anthomen, and T. A. Jones. 1995. Crystallographic and molecular-modeling studies of lipase B from Candida antarctica reveal a stereospecifi city pocket for secondary alcohols. Biochemistry. 34 : 16838 - 16851.
16. Martinelle, M., M. Holmquist, and K. Hult. 1995. On the interfacial activation of Candida antarctica lipase A and B as compared with Humicola lanuginosa lipase. Biochim. Biophys. Acta. 1258 : 272 - 276.
17. Trodler, P., and J. Pleiss. 2008. Modeling structure and fl exibility of Candida antarctica lipase B in organic solvents. BMC Struct. Biol. 8 : 9.
18. Skjøt, M., L. De Maria, R. Chatterjee, A. Svendsen, S. A. Patkar, P. R. Østergaard, and J. Brask. 2009. Understanding the plasticity of the alpha/beta hydrolase fold: lid swapping on the Candida antarctica lipase B results in chimeras with interesting biocatalytic properties. ChemBioChem. 10 : 520 - 527.
19. Ganjalikhany, M. R., B. Ranjbar, A. H. Taghavi, and T. T. Moghadam. 2012. Functional motions of Candida antarctica lipase B: A survey through open-close conformations. PLoS One. 7 : e40327.
20. Ferrario, V., C. Ebert, L. Knapic, D. Fattor, A. Basso, P. Spizzo, and L. Gardossi. 2011. Conformational changes of lipases in aqueous media: A comparative computational study and experimental implications. Adv. Synth. Catal. 353 : 2466 - 2480.
21. Fisher, S. J., J. Wilkinson, R. H. Henchman, and J. R. Helliwell. 2009. An evaluation review of the prediction of protonation states in proteins versus crystallographic experiment. Crystallogr. Rev. 15 : 231 - 259.
22. Fisher, S. J., M. P. Blakeley, M. Cianci, S. McSweeney, and J. R. Helliwell. 2012. Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness. Acta Crystallogr. D Biol. Crystallogr. 68 : 800 - 809.
23. Kabsch, W. 2010. XDS. Acta Crystallogr. D Biol. Crystallogr. 66 : 125 - 132.
24. Vagin, A., and A. Teplyakov. 1997. MOLREP: An automated program for molecular replacement. J. Appl. Crystallogr. 30 : 1022 - 1025.
25. Murshudov, G. N., A. A. Vagin, and E. J. Dodson. 1997. Refi nement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53 : 240 - 255.
26. Emsley, P., B. Lohkamp, W. G. Scott, and K. Cowtan. 2010. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66 : 486 - 501.
27. Joosten, R. P., F. Long, G. N. Murshudov, and A. Perrakis. 2014. The PDB-REDO server for macromolecular structure model optimization. IUCrJ. 1 : 213 - 220.
28. Winn, M. D., C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R. Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, et al. 2011. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67 : 235 - 242.
29. Uppenberg, J., S. Patkar, T. Bergfors, and T. A. Jones. 1994. Crystallization and preliminary X-ray studies of lipase B from Candida antarctica. J. Mol. Biol. 235 : 790 - 792.
30. Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 : 283 - 291.
31. Cruickshank, D. W. J. 1999. Remarks about protein structure precision. Acta Crystallogr. D Biol. Crystallogr. 55 : 583 - 601.
32. Prangé, T., M. Schiltz, L. Pernot, N. Colloc'h, S. Longhi, W. Bourguet, and R. Fourme. 1998. Exploring hydrophobic sites in proteins with xenon or krypton. Proteins. 30 : 61 - 73.
33. Olczak, A., M. Cianci, Q. Hao, P. J. Rizkallah, J. Raftery, and J. R. Helliwell. 2003. S-SWAT (softer single-wavelength anomalous technique): potential in high-throughput protein crystallography. Acta Crystallogr. A. 59 : 327 - 334.
34. Frey, P. A., S. A. Whitt, and J. B. Tobin. 1994. A low-barrier hydrogen bond in the catalytic triad of serine proteases. Science. 264 : 1927 - 1930.
35. Kuhn, P., M. Knapp, S. M. Soltis, G. Ganshaw, M. Thoene, and R. Bott. 1998. The 0.78 Å structure of a serine protease: Bacillus lentus subtilisin. Biochemistry. 37 : 13446 - 13452.
36. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25 : 3389 - 3402.
37. Derewenda, U., L. Swenson, Y. Wei, R. Green, P. M. Kobos, R. Joerger, M. J. Haas, and Z. S. Derewenda. 1994. Conformational lability of lipases observed in the absence of an oil-water interface: crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar. J. Lipid Res. 35 : 524 - 534.
38. Schrag, J. D., Y. Li, M. Cygler, D. Lang, T. Burgdorf, H-J. Hecht, R. Schmid, D. Schomburg, T. J. Rydel, J. D. Oliver, et al. 1997. The open conformation of a Pseudomonas lipase. Structure. 5 : 187 - 202.
39. Louwrier, A., G. J. Drtina, and A. M. Klibanov. 1996. On the issue of interfacial activation of lipase in nonaqueous media. Biotechnol. Bioeng. 50 : 1 - 5.
40. Laskowski, R. A. 2001. PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res. 29 : 221 - 222.
41. DeLano, W. L. 2002. The PyMOL User's Manual. DeLano Scientific, San Carlos, CA.
42. McNicholas, S., E. Potterton, K. S. Wilson, and M. E. Noble. 2011. Presenting your structures: The CCP4mg molecular-graphics software. Acta Crystallogr. D Biol. Crystallogr. 67 : 386 - 394.