Structural studies of a thermophilic esterase from a new Planctomycetes species, Thermogutta terrifontis

FEBS Journal

Volumn 282, Issue 15, 2015, Pages 2846-2857

  Sayer, Christopher ^a   Isupov, Michail N ^a   Bonch Osmolovskaya, Elizaveta ^b   Littlechild, Jennifer A ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

^b WINOGRADSKY INSTITUTE OF MICROBIOLOGY   (Russian Federation)

Author keywords

carboxyl esterase; Planctomyces; site directed mutagenesis; thermophile; X ray structure

Indexed keywords

ESTERASE; LIGAND;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME SPECIFICITY; ENZYME STABILITY; LIGAND BINDING; NONHUMAN; PLANCTOMYCETES; PRIORITY JOURNAL; PROTEIN EXPRESSION; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS; THERMOGUTTA TERRIFONTIS; BACTERIUM; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; PH; PROTEIN CONFORMATION; PROTEIN FOLDING; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PLANCTOMYCES; PLANCTOMYCETES;

BACTERIA; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; ESTERASES; HYDROGEN-ION CONCENTRATION; LIGANDS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 84938199369     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.13326     Document Type: Article

References (48)

1. Faber K, (1997) Biotransformations of non-natural compounds: state of the art and future developments. Pure Appl Chem 69, 1613-1632.
2. Montella IR, Schama R, &, Valle D, (2012) The classification of esterases: an important gene family involved in insecticide resistance-a review. Mem Inst Oswaldo Cruz 107, 437-449.
3. Bornscheuer UT, (2002) Microbial carboxyl esterases: classification, properties and application in biocatalysis. FEMS Microbiol Rev 26, 73-81.
4. de Vries RP, &, Visser J, (1999) Regulation of the feruloyl esterase (faeA) gene from Aspergillus niger. Appl Environ Microbiol 65, 5500-5503.
5. Jones RM, Collier LS, Neidle EL, &, Williams PA, (1999) Are ABC genes determine the catabolism of aryl esters in Acinetobacter sp. Strain ADP1. J Bacteriol 181, 4568-4575.
6. Sussman JL, Harel M, Frolow F, Oefher C, Goldman A, Toker L, &, Silman I, (1991) Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein. Science 253, 872-879.
7. Quax WJ, &, Broekhuizen CP, (1994) Development of a new Bacillus carboxyl esterase for use in the resolution of chiral drugs. Appl Microbiol Biotechnol 41, 425-431.
8. Schrag J, &, Cygler M, (1997) Lipases and alpha/beta hydrolase fold. Methods Enzymol 284, 85-107.
9. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, et al,. (1992) The α/β hydrolase fold. Protein Eng 5, 197-211.
10. Heikinheimo P, Goldman A, Jeffries C, &, Ollis DW, (1999) Of barn owls and bankers: a lush variety of α/β hydrolases. Structure 7, 141-146.
11. Wei Y, Schottel JL, Derewenda U, Swenson L, Patkar S, &, Derewenda ZS, (1995) A novel variant of the catalytic triad in the Streptomyces scabies esterase. Nat Struct Biol 2, 218-223.
12. Wagner UG, Petersen EI, Schwab H, &, Kratky C, (2002) EstB from Burkholderia gladioli: a novel esterase with a β-lactamase fold reveals steric factors to discriminate between esterolytic and β-lactam cleaving activity. Protein Sci 11, 467-478.
13. Isupov MN, Brindley AA, Hollingsworth EJ, Murshudov GN, Vagin AA, &, Littlechild JA, (2004) Crystallization and preliminary X-ray diffraction studies of a fungal hydrolase from Ophiostoma novo-ulmi. Acta Crystallogr D Biol Crystallogr 60, 879-882.
14. Blow DM, Birktoft JJ, &, Hartley BS, (1969) Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 221, 337-340.
15. Nardini M, &, Dijkstra BW, (1999) Alpha/beta hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 9, 732-737.
16. Bourne PC, Isupov MN, &, Littlechild JA, (2000) The atomic-resolution structure of a novel bacterial esterase. Structure 8, 143-151.
17. Slobodkina GB, Kovaleva OL, Miroshnichenko ML, Slobodkin AI, Kolganova TV, Novikov AA, van Heerden E, &, Bonch-Osmolovskaya EA, (2014) Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., novel thermophilic anaerobic representatives of the phylum Planctomycetes. Int J Syst Evol Microbiol 65, 760-765.
18. Richardson JS, (1981) The anatomy and taxonomy of protein structure. Adv Prot Chem 34, 167-339.
19. Stewart PDS, Kolek SA, Briggs RA, Chayen NE, &, Baldock PFM, (2011) Random microseeding: a theoretical and practical exploration of seed stability and seeding techniques for successful protein crystallization. Cryst Growth Des 11, 3432-3441.
20. Carr PD, &, Ollis DL, (2009) Alpha/beta hydrolase fold: an update. Protein Pept Lett 16, 1137-1148.
21. Marchot P, &, Chatonnet A, (2012) Enzymatic activity and protein interactions in alpha/beta hydrolase fold proteins: moonlighting versus promiscuity. Protein Pept Lett 19, 132-143.
22. Altschul S, Gish W, Miller W, Myers E, &, Lipman D, (1990) Basic local alignment search tool. J Mol Biol 215, 403-410.
23. Bains J, Kaufman L, Farnell B, &, Boulanger MJ, (2011) A product analog bound form of 3-oxoadipate-enol-lactonase (PcaD) reveals a multifunctional role for the divergent cap domain. J Mol Biol 406, 649-658.
24. Yin DL, Bernhardt P, Morley KL, Jiang Y, Cheeseman JD, Purpero V, Schrag JD, &, Kazlauskas RJ, (2010) Switching catalysis from hydrolysis to perhydrolysis in P. fluorescens esterase. Biochemistry 49, 1931-1942.
25. Line K, Isupov MN, &, Littlechild JA, (2004) The crystal structure of a (-) gamma-lactamase from an Aureobacterium species reveals a tetrahedral intermediate in the active site. J Mol Biol 338, 519-532.
26. Hofmann B, Tölzer S, Pelletier I, Altenbuchner J, van Pée KH, &, Hecht HJ, (1998) Structural investigation of the cofactor-free chloroperoxidases. J Mol Biol 279, 889-900.
27. Cheeseman JD, Tocilj A, Park S, Schrag JD, &, Kazlauskas RJ, (2004) Structure of an aryl esterase from Pseudomonas fluorescens. Acta Crystallogr D Biol Crystallogr 60, 1237-1243.
28. Line K, (2004) Studies on novel industrial ?-lactamase enzymes. PhD thesis. Exeter University, UK.
29. Pilalis E, Ladoukakis E, Kolisis F, &, Chatziioannou A, (2012) A Galaxy workflow for the functional annotation of metagenomic samples. In: ' Artificial Intelligence: Theories and Applications.' (, Maglogiannis I, Plagianakos V, &, Vlahavas I, eds), pp. 247-253. Springer, Berlin Heidelberg, 7297.
30. Ladoukakis E, Pilalis E, Chatziioannou A, &, Kolisis F, (2014) ANASTASIA a versatile web platform for metagenomic analysis. New Biotechnol 31, S170.
31. Armstrong JM, Myers DV, Verpoorte JA, &, Edsall JT, (1966) Purification and properties of human erythrocyte carbonic anhydrases. J Biol Chem 241, 5137-5149.
32. Hiblot J, Gotthard G, Chabriere E, &, Elias M, (2012) Structural and enzymatic characterization of the lactonase SisLac from Sulfolobus islandicus. PLoS One 7, e47028.
33. Kabsch W, (2010) XDS. Acta Crystallogr D Biol Crystallogr 66, 125-132.
34. Evans PR, &, Murshudov GN, (2013) How good are my data and what is the resolution? Acta Crystallogr D Biol Crystallogr 69, 1204-1214.
35. Winter G, Lobley CMC, &, Prince SM, (2013) Decision making in xia2. Acta Crystallogr D Biol Crystallogr 69, 1260-1273.
36. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, et al,. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67, 235-242.
37. Vagin A, &, Teplyakov A, (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66, 22-25.
38. Lebedev AA, Vagin AA, &, Murshudov GN, (2008) Model preparation in MOLREP and examples of model improvement using X-ray data. Acta Crystallogr D Biol Crystallogr 64, 33-39.
39. Langer GG, Hazledine S, Wiegels T, Carolan C, &, Lamzin VS, (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr 69, 635-641.
40. Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, &, Vagin AA, (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67, 355-367.
41. Thorn A, &, Sheldrick GM, (2013) Extending molecular-replacement solutions with SHELXE. Acta Crystallogr D Biol Crystallogr 69, 2251-2256.
42. Emsley P, Lohkamp B, Scott WG, &, Cowtan K, (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66, 486-501.
43. Lebedev AA, Young P, Isupov MN, Moroz OV, Vagin AA, &, Murshudov GN, (2012) JLigand: a graphical tool for the CCP4 template-restraint library. Acta Crystallogr D Biol Crystallogr 68, 431-440.
44. Laskowski RA, MacArthur MW, Moss DS, &, Thornton JM, (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291.
45. DeLano WL, (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org.
46. Vaguine AA, Richelle J, &, Wodak SJ, (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 55, 191-205.
47. Laskowski RA, &, Swindells MB, (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51, 2778-2786.
48. Potterton L, McNicholas S, Krissinel E, Gruber J, Cowtan K, Emsley P, Murshudov GN, Cohen S, Perrakis A, &, Noble M, (2004) Developments in the CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr 60, 2288-2294.