An inserted α/β subdomain shapes the catalytic pocket of lactobacillus johnsonii cinnamoyl esterase

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Lai, Kin Kwan ^a   Stogios, Peter J ^b   Vu, Clara ^a   Xu, Xiaohui ^b   Cui, Hong ^b   Molloy, Sara ^a   Savchenko, Alexei ^b   Yakunin, Alexander ^b   Gonzalez, Claudio F ^a  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; BACTERIAL ENZYME; HISTIDINE; LJ0536; SERINE; UNCLASSIFIED DRUG; ALANINE; CARBOXYLESTERASE; MUTANT PROTEIN;

ALPHA CHAIN; AMINO ACID SEQUENCE; ARTICLE; BETA CHAIN; CANONICAL ANALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME SUBSTRATE COMPLEX; ENZYME SYNTHESIS; LACTOBACILLUS JOHNSONII; LIGAND BINDING; NONHUMAN; PROTEIN DATA BANK; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; STRUCTURE ANALYSIS; BINDING SITE; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; HUMAN; HYDROLYSIS; KINETICS; LACTOBACILLUS; METABOLISM; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; STRUCTURAL HOMOLOGY; STRUCTURE ACTIVITY RELATION; X RAY DIFFRACTION;

BACTERIA (MICROORGANISMS); LACTOBACILLUS JOHNSONII;

ALANINE; BINDING SITES; BIOCATALYSIS; CARBOXYLIC ESTER HYDROLASES; CATALYTIC DOMAIN; HUMANS; HYDROLYSIS; KINETICS; LACTOBACILLUS; MODELS, MOLECULAR; MUTAGENESIS, INSERTIONAL; MUTAGENESIS, SITE-DIRECTED; MUTANT PROTEINS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SERINE; STRUCTURAL HOMOLOGY, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; X-RAY DIFFRACTION;

EID: 80051856617     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023269     Document Type: Article

References (53)

1. Choo W, Birch E, (2009) Radical scavenging activity of lipophilized products from lipase-catalyzed transesterification of triolein with cinnamic and ferulic acids. Lipids 44: 145-152.
2. Chao P, Hsu C, Yin M, (2009) Anti-inflammatory and anti-coagulatory activities of caffeic acid and ellagic acid in cardiac tissue of diabetic mice. Nutr Metab (Lond) 6: 33.
3. Srinivasan M, Sudheer A, Menon V, (2007) Ferulic Acid: therapeutic potential through its antioxidant property. J Clin Biochem Nutr 40: 92-100.
4. Hanhineva K, Törrönen R, Bondia-Pons I, Pekkinen J, Kolehmainen M, et al. (2010) Impact of dietary polyphenols on carbohydrate metabolism. Int J Mol Sci 11: 1365-1402.
5. Cho A, Jeon S, Kim M, Yeo J, Seo K, et al. (2010) Chlorogenic acid exhibits anti-obesity property and improves lipid metabolism in high-fat diet-induced-obese mice. Food Chem Toxicol 48: 937-943.
6. Crozier A, Jaganath I, Clifford M, (2009) Dietary phenolics: chemistry, bioavailability and effects on health. Nat Prod Rep 26: 1001-1043.
7. Jemai H, El Feki A, Sayadi S, (2009) Antidiabetic and antioxidant effects of hydroxytyrosol and oleuropein from olive leaves in alloxan-diabetic rats. J Agric Food Chem 57: 8798-8804.
8. Clifford MN, (2000) Chlorogenic acids and other cinnamates- nature, occurrence, dietary burden, absorption and metabolism. J Sci Food Agric 80: 1033-1043.
9. Konishi Y, Hitomi Y, Yoshida M, Yoshioka E, (2005) Pharmacokinetic study of caffeic and rosmarinic acids in rats after oral administration. J Agric Food Chem 53: 4740-4746.
10. Konishi Y, Kobayashi S, (2005) Transepithelial transport of rosmarinic acid in intestinal Caco-2 cell monolayers. Biosci Biotechnol Biochem 69: 583-591.
11. Kroon PA, Faulds CB, Ryden P, Robertson JA, Williamson G, (1997) Release of Covalently Bound Ferulic Acid from Fiber in the Human Colon. J Agric Food Chem 45: 661-667.
12. Karlsson P, Huss U, Jenner A, Halliwell B, Bohlin L, et al. (2005) Human fecal water inhibits COX-2 in colonic HT-29 cells: role of phenolic compounds. J Nutr 135: 2343-2349.
13. Andreasen M, Kroon P, Williamson G, Garcia-Conesa M, (2001) Esterase activity able to hydrolyze dietary antioxidant hydroxycinnamates is distributed along the intestine of mammals. J Agric Food Chem 49: 5679-5684.
14. Lai K, Lorca G, Gonzalez C, (2009) Biochemical properties of two cinnamoyl esterases purified from a Lactobacillus johnsonii strain isolated from stool samples of diabetes-resistant rats. Appl Environ Microbiol 75: 5018-5024.
15. Roesch L, Lorca G, Casella G, Giongo A, Naranjo A, et al. (2009) Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model. ISME J 3: 536-548.
16. Valladares R, Sankar D, Li N, Williams E, Lai K, et al. (2010) Lactobacillus johnsonii N6.2 mitigates the development of type 1 diabetes in BB-DP rats. PLoS One 5: e10507.
17. Benoit I, Asther M, Bourne Y, Navarro D, Canaan S, et al. (2007) Gene overexpression and biochemical characterization of the biotechnologically relevant chlorogenic acid hydrolase from Aspergillus niger. Appl Environ Microbiol 73: 5624-5632.
18. Faulds C, Molina R, Gonzalez R, Husband F, Juge N, et al. (2005) Probing the determinants of substrate specificity of a feruloyl esterase, AnFaeA, from Aspergillus niger. FEBS J 272: 4362-4371.
19. Hermoso J, Sanz-Aparicio J, Molina R, Juge N, González R, et al. (2004) The crystal structure of feruloyl esterase A from Aspergillus niger suggests evolutive functional convergence in feruloyl esterase family. J Mol Biol 338: 495-506.
20. Goldstone D, Villas-Bôas S, Till M, Kelly W, Attwood G, et al. (2010) Structural and functional characterization of a promiscuous feruloyl esterase (Est1E) from the rumen bacterium Butyrivibrio proteoclasticus. Proteins 78: 1457-1469.
21. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, et al. (1992) The alpha/beta hydrolase fold. Protein Eng 5: 197-211.
22. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, (2011) GenBank. Nucleic Acids Res 39: D32-D37.
23. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
24. Holm L, Rosenström P, (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545-549.
25. Bertrand T, Augé F, Houtmann J, Rak A, Vallée F, et al. (2010) Structural basis for human monoglyceride lipase inhibition. J Mol Biol 396: 663-673.
26. Hofmann B, Tölzer S, Pelletier I, Altenbuchner J, van Pée KH, et al. (1998) Structural investigation of the cofactor-free chloroperoxidases. J Mol Biol 279: 889-900.
27. Yin dL, Bernhardt P, Morley KL, Jiang Y, Cheeseman JD, et al. (2010) Switching catalysis from hydrolysis to perhydrolysis in Pseudomonas fluorescens esterase. Biochemistry 49: 1931-1942.
28. Lai L, Xu Z, Zhou J, Lee K, Amidon G, (2008) Molecular basis of prodrug activation by human valacyclovirase, an alpha-amino acid ester hydrolase. J Biol Chem 283: 9318-9327.
29. Gonzalez C, Proudfoot M, Brown G, Korniyenko Y, Mori H, et al. (2006) Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem 281: 14514-14522.
30. Smith A, Müller R, Toscano M, Kast P, Hellinga H, et al. (2008) Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle. J Am Chem Soc 130: 15361-15373.
31. Schubot FD, Kataeva IA, Blum DL, Shah AK, Ljungdahl LG, et al. (2001) Structural basis for the substrate specificity of the feruloyl esterase domain of the cellulosomal xylanase Z from Clostridium thermocellum. Biochemistry 40: 12524-12532.
32. Ekici O, Paetzel M, Dalbey R, (2008) Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration. Protein Sci 17: 2023-2037.
33. Kim I, Chu X, Kim S, Provoda C, Lee K, et al. (2003) Identification of a human valacyclovirase: biphenyl hydrolase-like protein as valacyclovir hydrolase. J Biol Chem 278: 25348-25356.
34. Udatha DB, Kouskoumvekaki I, Olsson L, Panagiotou G, (2011) The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases. Biotechnol Adv 29: 94-110.
35. Dalrymple B, Swadling Y, Cybinski D, Xue G, (1996) Cloning of a gene encoding cinnamoyl ester hydrolase from the ruminal bacterium Butyrivibrio fibrisolvens E14 by a novel method. FEMS Microbiol Lett 143: 115-120.
36. Lorca G, Ezersky A, Lunin V, Walker J, Altamentova S, et al. (2007) Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli IclR transcriptional regulator. J Biol Chem 282: 16476-16491.
37. Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, et al. (2007) In situ proteolysis for protein crystallization and structure determination. Nat Methods 4: 1019-1021.
38. Kimber MS, Vallee F, Houston S, Necakov A, Skarina T, et al. (2003) Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens. Proteins 51: 562-568.
39. Hope H, (1988) Cryocrystallography of biological macromolecules: a generally applicable method. Acta Crystallogr B 44 (Pt 1): 22-26.
40. Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. In: Charles WCarter, editors. Methods Enzymol Academic Press pp. 307-326.
41. McCoy A, Grosse-Kunstleve R, Adams P, Winn M, Storoni L, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658-674.
42. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
43. Murshudov G, Vagin A, Dodson E, (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240-255.
44. Adams P, Afonine P, Bunkóczi G, Chen V, Davis I, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213-221.
45. Blanc E, Roversi P, Vonrhein C, Flensburg C, Lea S, et al. (2004) Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Crystallogr D Biol Crystallogr 60: 2210-2221.
46. Painter J, Merritt EA, (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr 62: 439-450.
47. Schüttelkopf A, van Aalten D, (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 60: 1355-1363.
48. Laskowski RA, MacArthur MW, Moss DS, Thornton JM, (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283-291.
49. Chen V, Arendall Wr, Headd J, Keedy D, Immormino R, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12-21.
50. Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
51. DeLano WL, (2002) The PyMOL Molecular Graphics System, version 1.00 Schrödinger, LLC.
52. Mastihuba V, Kremnický L, Mastihubová M, Willett J, Côté G, (2002) A spectrophotometric assay for feruloyl esterases. Anal Biochem 309: 96-101.
53. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.