Structural Redesign of Lipase B from Candida antarctica by Circular Permutation and Incremental Truncation

Journal of Molecular Biology

Volumn 393, Issue 1, 2009, Pages 191-201

  Qian, Zhen ^a   Horton, John R ^b   Cheng, Xiaodong ^b   Lutz, Stefan ^a  

^a EMORY UNIVERSITY   (United States)

^b EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Candida antartica lipase B; circular permutation; enzyme engineering; incremental truncation

Indexed keywords

AMINO ACID; DIMER; ENZYME VARIANT; HOMODIMER; HYDROLASE; LIPASE B; MONOMER; PHOSPHONIC ACID DERIVATIVE;

AMINO TERMINAL SEQUENCE; ARTICLE; CANDIDA ANTARCTICA; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME METABOLISM; ENZYME SUBSTRATE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; TEMPERATURE; X RAY CRYSTALLOGRAPHY;

CANDIDA; CANDIDA ANTARCTICA;

EID: 70349255505     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.08.008     Document Type: Article

References (52)

1. Berglund P. Controlling lipase enantioselectivity for organic synthesis. Biomol. Eng. 18 (2001) 13-22
2. Bornscheuer U.T., Bessler C., Srinivas R., and Krishna S.H. Optimizing lipases and related enzymes for efficient application. Trends Biotechnol. 20 (2002) 433-437
3. Bornscheuer U.T., and Kazlauskas R.J. Hydrolases in Organic Synthesis-Regio- and Stereoselective Biotransformations (1999), Wiley-VCH, Weinheim, Germany
4. Freemantle M. Biocatalysis in polymer science. Chem. Eng. News 82 (2004) 25-27
5. Jaeger K.E., and Eggert T. Lipases for biotechnology. Curr. Opin. Biotechnol. 13 (2002) 390-397
6. Fjerbaek L., Christensen K.V., and Norddahl B. A review of the current state of biodiesel production using enzymatic transesterification. Biotechnol. Bioeng. 102 (2009) 1298-1315
7. Uppenberg J., Hansen M.T., Patkar S., and Jones T.A. The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica. Structure 2 (1994) 293-308
8. Uppenberg J., Ohrner N., Norin M., Hult K., Kleywegt G.J., Patkar S., et al. Crystallographic and molecular-modeling studies of lipase B from Candida antarctica reveal a stereospecificity pocket for secondary alcohols. Biochemistry 34 (1995) 16838-16851
9. Suen W.C., Zhang N., Xiao L., Madison V., and Zaks A. Improved activity and thermostability of Candida antarctica lipase B by DNA family shuffling. Protein Eng. Des. Sel. 17 (2004) 133-140
10. Zhang N., Suen W.C., Windsor W., Xiao L., Madison V., and Zaks A. Improving tolerance of Candida antarctica lipase B towards irreversible thermal inactivation through directed evolution. Protein Eng. 16 (2003) 599-605
11. Rotticci D., Rotticci-Mulder J.C., Denman S., Norin T., and Hult K. Improved enantioselectivity of a lipase by rational protein engineering. ChemBioChem 2 (2001) 766-770
12. Magnusson A.O., Rotticci-Mulder J.C., Santagostino A., and Hult K. Creating space for large secondary alcohols by rational redesign of Candida antarctica lipase B. ChemBioChem 6 (2005) 1051-1056
13. Skjot M., De Maria L., Chatterjee R., Svendsen A., Patkar S.A., Ostergaard P.R., and Brask J. 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 (2009) 520-527
14. Kim S.Y., Sohn J.H., Pyun Y.R., Yang I.S., Kim K.H., and Choi E.S. In vitro evolution of lipase B from Candida antarctica using surface display in hansenula polymorpha. J. Microbiol. Biotechnol. 17 (2007) 1308-1315
15. Qian Z., and Lutz S. Improving the catalytic activity of Candida antarctica lipase B by circular permutation. J. Am. Chem. Soc. 127 (2005) 13466-13467
16. Hisano T., Kasuya K.I., Tezuka Y., Ishii N., Kobayashi T., Shiraki M., et al. The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters. J. Mol. Biol. 356 (2006) 993-1004
17. Weiner III J., and Bornberg-Bauer E. Evolution of circular permutations in multidomain proteins. Mol. Biol. Evol. 23 (2006) 734-743
18. Jeltsch A. Circular permutations in the molecular evolution of DNA methyltransferases. J. Mol. Evol. 49 (1999) 161-164
19. Zhang T., Bertelsen E., Benvegnu D., and Alber T. Circular permutation of T4 lysozyme. Biochemistry 32 (1993) 12311-12318
20. Hennecke J., Sebbel P., and Glockshuber R. Random circular permutation of DsbA reveals segments that are essential for protein folding and stability. J. Mol. Biol. 286 (1999) 1197-1215
21. Viguera A.R., Blanco F.J., and Serrano L. The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. J. Mol. Biol. 247 (1995) 670-681
22. Zhang P., and Schachman H.K. In vivo formation of allosteric aspartate transcarbamoylase containing circularly permuted catalytic polypeptide chains: implications for protein folding and assembly. Protein Sci. 5 (1996) 1290-1300
23. Iwakura M., Nakamura T., Yamane C., and Maki K. Systematic circular permutation of an entire protein reveals essential folding elements. Nat. Struct. Biol. 7 (2000) 580-585
24. Lindberg M., Tangrot J., and Oliveberg M. Complete change of the protein folding transition state upon circular permutation. Nat. Struct. Biol. 9 (2002) 818-822
25. Baird G.S., Zacharias D.A., and Tsien R.Y. Circular permutation and receptor insertion within green fluorescent proteins. Proc. Natl Acad. Sci. USA 96 (1999) 11241-11246
26. Ostermeier M. Engineering allosteric protein switches by domain insertion. Protein Eng. Des. Sel. 18 (2005) 359-364
27. Qian Z., Fields C.J., and Lutz S. Investigating the structural and functional consequences of circular permutation on lipase B from Candida antarctica. ChemBioChem 8 (2007) 1989-1996
28. Ay J., Hahn M., Decanniere K., Piotukh K., Borriss R., and Heinemann U. Crystal structures and properties of de novo circularly permuted 1,3-1,4-beta-glucanases. Proteins 30 (1998) 155-167
29. Chu V., Freitag S., Le Trong I., Stenkamp R.E., and Stayton P.S. Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system. Protein Sci. 7 (1998) 848-859
30. Manjasetty B.A., Hennecke J., Glockshuber R., and Heinemann U. Structure of circularly permuted DsbA(Q100T99): preserved global fold and local structural adjustments. Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 (2004) 304-309
31. Tougard P., Bizebard T., Ritco-Vonsovici M., Minard P., and Desmadril M. Structure of a circularly permuted phosphoglycerate kinase. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58 (2002) 2018-2023
32. Pieper U., Hayakawa K., Li Z., and Herzberg O. Circularly permuted beta-lactamase from Staphylococcus aureus PC1. Biochemistry 36 (1997) 8767-8774
33. Nagi A.D., and Regan L. An inverse correlation between loop length and stability in a four-helix-bundle protein. Folding Des. 2 (1997) 67-75
34. Wang L., Rivera E.V., Benavides-Garcia M.G., and Nall B.T. Loop entropy and cytochrome c stability. J. Mol. Biol. 353 (2005) 719-729
35. Lutz S., Ostermeier M., and Benkovic S.J. Rapid generation of incremental truncation libraries for protein engineering using alpha-phosphothioate nucleotides. Nucleic Acids Res. 29 (2001) E16
36. Lutz S., and Ostermeier M. Preparation of SCRATCHY hybrid protein libraries: size- and in-frame selection of nucleic acid sequences. Methods Mol. Biol. 231 (2003) 143-151
37. Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372 (2007) 774-797
38. Fersht A.R. The hydrogen bond in molecular recognition. Trends Biochem. Sci. 12 (1987) 301-304
39. Janin J., Miller S., and Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204 (1988) 155-164
40. Lutz S. Engineering lipase B from Candida antarctica. Tetrahedron: Asymmetry 15 (2004) 2743-2748
41. Trodler P., and Pleiss J. Modeling structure and flexibility of Candida antarctica lipase B in organic solvents. BMC Struct. Biol. 8 (2008) 9
42. Schlunegger M.P., Bennett M.J., and Eisenberg D. Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Adv. Protein Chem. 50 (1997) 61-122
43. Raag R., and Whitlow M. Single-chain Fvs. FASEB J. 9 (1995) 73-80
44. Green S.M., Gittis A.G., Meeker A.K., and Lattman E.E. One-step evolution of a dimer from a monomeric protein. Nat. Struct. Biol. 2 (1995) 746-751
45. Bencharit S., Morton C.L., Xue Y., Potter P.M., and Redinbo M.R. Structural basis of heroin and cocaine metabolism by a promiscuous human drug-processing enzyme. Nat. Struct. Biol. 10 (2003) 349-356
46. Stubbe J., Tian J., He A., Sinskey A.J., Lawrence A.G., and Liu P. Nontemplate-dependent polymerization processes: polyhydroxyalkanoate synthases as a paradigm. Annu. Rev. Biochem. 74 (2005) 433-480
47. Peisajovich S.G., Rockah L., and Tawfik D.S. Evolution of new protein topologies through multistep gene rearrangements. Nat. Genet. 38 (2006) 168-174
48. Grishin N.V. Fold change in evolution of protein structures. J. Struct. Biol. 134 (2001) 167-185
49. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. 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
50. Ottosson J., Rotticci-Mulder J.C., Rotticci D., and Hult K. Rational design of enantioselective enzymes requires considerations of entropy. Protein Sci. 10 (2001) 1769-1774
51. Tong L., and Rossmann M.G. Rotation function calculations with GLRF program. Methods Enzymol. 276 (1997) 594-611
52. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 905-921