3g02 › Citations

Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage.

Reetz MT, Bocola M, Wang LW, Sanchis J, Cronin A, Arand M, Zou J, Archelas A, Bottalla AL, Naworyta A, Mowbray SL
J Am Chem Soc 131 7334-43 (2009)
Related entries: 1qo7, 3g0i

Cited: 64 times
EuropePMC logo PMID: 19469578

Abstract

Directed evolution of enzymes as enantioselective catalysts in organic chemistry is an alternative to traditional asymmetric catalysis using chiral transition-metal complexes or organocatalysts, the different approaches often being complementary. Moreover, directed evolution studies allow us to learn more about how enzymes perform mechanistically. The present study concerns a previously evolved highly enantioselective mutant of the epoxide hydrolase from Aspergillus niger in the hydrolytic kinetic resolution of racemic glycidyl phenyl ether. Kinetic data, molecular dynamics calculations, molecular modeling, inhibition experiments, and X-ray structural work for the wild-type (WT) enzyme and the best mutant reveal the basis of the large increase in enantioselectivity (E = 4.6 versus E = 115). The overall structures of the WT and the mutant are essentially identical, but dramatic differences are observed in the active site as revealed by the X-ray structures. All of the experimental and computational results support a model in which productive positioning of the preferred (S)-glycidyl phenyl ether, but not the (R)-enantiomer, forms the basis of enhanced enantioselectivity. Predictions regarding substrate scope and enantioselectivity of the best mutant are shown to be possible.

Articles - 3g02 mentioned but not cited (5)

  1. Pseudomonas aeruginosa Cif defines a distinct class of α/β epoxide hydrolases utilizing a His/Tyr ring-opening pair. Bahl CD, Madden DR. Protein Pept Lett 19 186-193 (2012)
  2. The ATGL lipase cooperates with ABHD5 to mobilize lipids for hepatitis C virus assembly. Vieyres G, Reichert I, Carpentier A, Vondran FWR, Pietschmann T. PLoS Pathog 16 e1008554 (2020)
  3. Cloning and Characterization of Drosophila melanogaster Juvenile Hormone Epoxide Hydrolases (JHEH) and Their Promoters. Borovsky D, Breyssens H, Buytaert E, Peeters T, Laroye C, Stoffels K, Rougé P. Biomolecules 12 991 (2022)
  4. Simple Selection Procedure to Distinguish between Static and Flexible Loops. Mitusińska K, Skalski T, Góra A. Int J Mol Sci 21 2293 (2020)
  5. Design of a Microbial Remediation Inoculation Program for Petroleum Hydrocarbon Contaminated Sites Based on Degradation Pathways. Li X, He W, Du M, Zheng J, Du X, Li Y. Int J Environ Res Public Health 18 8794 (2021)


Reviews citing this publication (11)

  1. Directed evolution drives the next generation of biocatalysts. Turner NJ. Nat Chem Biol 5 567-573 (2009)
  2. Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions. Reetz MT. Angew Chem Int Ed Engl 50 138-174 (2011)
  3. Industrial applications of enzyme biocatalysis: Current status and future aspects. Choi JM, Han SS, Kim HS. Biotechnol Adv 33 1443-1454 (2015)
  4. Biocatalyst development by directed evolution. Wang M, Si T, Zhao H. Bioresour Technol 115 117-125 (2012)
  5. A Retrosynthesis Approach for Biocatalysis in Organic Synthesis. de Souza ROMA, Miranda LSM, Bornscheuer UT. Chemistry 23 12040-12063 (2017)
  6. New opportunities for biocatalysis: driving the synthesis of chiral chemicals. Zheng GW, Xu JH. Curr Opin Biotechnol 22 784-792 (2011)
  7. Enzymes that catalyse SN2 reaction mechanisms. O'Hagan D, Schmidberger JW. Nat Prod Rep 27 900-918 (2010)
  8. Recent insights into the structure and function of comparative gene identification-58. Oberer M, Boeszoermenyi A, Nagy HM, Zechner R. Curr Opin Lipidol 22 149-158 (2011)
  9. Inverting hydrolases and their use in enantioconvergent biotransformations. Schober M, Faber K. Trends Biotechnol 31 468-478 (2013)
  10. Protein engineering for development of new hydrolytic biocatalysts. Widersten M. Curr Opin Chem Biol 21 42-47 (2014)
  11. Epoxide hydrolysis as a model system for understanding flux through a branched reaction scheme. Janfalk Carlsson Å, Bauer P, Dobritzsch D, Kamerlin SCL, Widersten M. IUCrJ 5 269-282 (2018)

Articles citing this publication (48)

  1. How mutational epistasis impairs predictability in protein evolution and design. Miton CM, Tokuriki N. Protein Sci 25 1260-1272 (2016)
  2. Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering. Prokop Z, Sato Y, Brezovsky J, Mozga T, Chaloupkova R, Koudelakova T, Jerabek P, Stepankova V, Natsume R, van Leeuwen JG, Janssen DB, Florian J, Nagata Y, Senda T, Damborsky J. Angew Chem Int Ed Engl 49 6111-6115 (2010)
  3. Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima. Gumulya Y, Sanchis J, Reetz MT. Chembiochem 13 1060-1066 (2012)
  4. Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates. Kong XD, Yuan S, Li L, Chen S, Xu JH, Zhou J. Proc Natl Acad Sci U S A 111 15717-15722 (2014)
  5. A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes. Cadet F, Fontaine N, Li G, Sanchis J, Ng Fuk Chong M, Pandjaitan R, Vetrivel I, Offmann B, Reetz MT. Sci Rep 8 16757 (2018)
  6. Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling. Lonsdale R, Hoyle S, Grey DT, Ridder L, Mulholland AJ. Biochemistry 51 1774-1786 (2012)
  7. Reshaping an enzyme binding pocket for enhanced and inverted stereoselectivity: use of smallest amino acid alphabets in directed evolution. Sun Z, Lonsdale R, Kong XD, Xu JH, Zhou J, Reetz MT. Angew Chem Int Ed Engl 54 12410-12415 (2015)
  8. Engineering the loops in a lipase for stability in DMSO. Yedavalli P, Rao NM. Protein Eng Des Sel 26 317-324 (2013)
  9. Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. Amrein BA, Bauer P, Duarte F, Janfalk Carlsson Å, Naworyta A, Mowbray SL, Widersten M, Kamerlin SC. ACS Catal 5 5702-5713 (2015)
  10. Focused directed evolution of pentaerythritol tetranitrate reductase by using automated anaerobic kinetic screening of site-saturated libraries. Hulley ME, Toogood HS, Fryszkowska A, Mansell D, Stephens GM, Gardiner JM, Scrutton NS. Chembiochem 11 2433-2447 (2010)
  11. Enhanced enantioselectivity of a carboxyl esterase from Rhodobacter sphaeroides by directed evolution. Ma J, Wu L, Guo F, Gu J, Tang X, Jiang L, Liu J, Zhou J, Yu H. Appl Microbiol Biotechnol 97 4897-4906 (2013)
  12. Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm. Feng X, Sanchis J, Reetz MT, Rabitz H. Chemistry 18 5646-5654 (2012)
  13. Organocatalytic asymmetric hydrolysis of epoxides. Monaco MR, Prévost S, List B. Angew Chem Int Ed Engl 53 8142-8145 (2014)
  14. Key residues for controlling enantioselectivity of Halohydrin dehalogenase from Arthrobacter sp. strain AD2, revealed by structure-guided directed evolution. Tang L, Zhu X, Zheng H, Jiang R, Majeric Elenkov M. Appl Environ Microbiol 78 2631-2637 (2012)
  15. Structural insights into substrate specificity in variants of N-acetylneuraminic Acid lyase produced by directed evolution. Campeotto I, Bolt AH, Harman TA, Dennis C, Trinh CH, Phillips SE, Nelson A, Pearson AR, Berry A. J Mol Biol 404 56-69 (2010)
  16. Mutations in salt-bridging residues at the interface of the core and lid domains of epoxide hydrolase StEH1 affect regioselectivity, protein stability and hysteresis. Lindberg D, Ahmad S, Widersten M. Arch Biochem Biophys 495 165-173 (2010)
  17. Redesign of enzyme for improving catalytic activity and enantioselectivity toward poor substrates: manipulation of the transition state. Ema T, Nakano Y, Yoshida D, Kamata S, Sakai T. Org Biomol Chem 10 6299-6308 (2012)
  18. Structural determinants for the stereoselective hydrolysis of chiral substrates by phosphotriesterase. Tsai PC, Fan Y, Kim J, Yang L, Almo SC, Gao YQ, Raushel FM. Biochemistry 49 7988-7997 (2010)
  19. A new dehydrogenase from Clostridium acetobutylicum for asymmetric synthesis: dynamic reductive kinetic resolution entry into the Taxotère side chain. Applegate GA, Cheloha RW, Nelson DL, Berkowitz DB. Chem Commun (Camb) 47 2420-2422 (2011)
  20. Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. Mitusińska K, Magdziarz T, Bzówka M, Stańczak A, Gora A. Biomolecules 8 E143 (2018)
  21. Laboratory evolution of an epoxide hydrolase - towards an enantioconvergent biocatalyst. Kotik M, Archelas A, Faměrová V, Oubrechtová P, Křen V. J Biotechnol 156 1-10 (2011)
  22. MDC-Analyzer: a novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites. Tang L, Wang X, Ru B, Sun H, Huang J, Gao H. Biotechniques 56 301-2, 304, 306-8, passim (2014)
  23. Modification of substrate specificity resulting in an epoxide hydrolase with shifted enantiopreference for (2,3-epoxypropyl)benzene. Gurell A, Widersten M. Chembiochem 11 1422-1429 (2010)
  24. New Thermophilic α/β Class Epoxide Hydrolases Found in Metagenomes From Hot Environments. Ferrandi EE, Sayer C, De Rose SA, Guazzelli E, Marchesi C, Saneei V, Isupov MN, Littlechild JA, Monti D. Front Bioeng Biotechnol 6 144 (2018)
  25. Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase. Hvorecny KL, Bahl CD, Kitamura S, Lee KSS, Hammock BD, Morisseau C, Madden DR. Structure 25 697-707.e4 (2017)
  26. Protein engineering of a nitrilase from Burkholderia cenocepacia J2315 for efficient and enantioselective production of (R)-o-chloromandelic acid. Wang H, Gao W, Sun H, Chen L, Zhang L, Wang X, Wei D. Appl Environ Microbiol 81 8469-8477 (2015)
  27. A unique mono- and diacylglycerol lipase from Penicillium cyclopium: heterologous expression, biochemical characterization and molecular basis for its substrate selectivity. Tan ZB, Li JF, Li XT, Gu Y, Wu MC, Wu J, Wang JQ. PLoS One 9 e102040 (2014)
  28. Efficient kinetic resolution of phenyl glycidyl ether by a novel epoxide hydrolase from Tsukamurella paurometabola. Wu K, Wang H, Sun H, Wei D. Appl Microbiol Biotechnol 99 9511-9521 (2015)
  29. Exploring the origins of selectivity in soluble epoxide hydrolase from Bacillus megaterium. Serrano-Hervás E, Garcia-Borràs M, Osuna S. Org Biomol Chem 15 8827-8835 (2017)
  30. Expression of a novel epoxide hydrolase of Aspergillus usamii E001 in Escherichia coli and its performance in resolution of racemic styrene oxide. Hu D, Tang CD, Yang B, Liu JC, Yu T, Deng C, Wu MC. J Ind Microbiol Biotechnol 42 671-680 (2015)
  31. The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. Denesyuk A, Dimitriou PS, Johnson MS, Nakayama T, Denessiouk K. PLoS One 15 e0229376 (2020)
  32. Epoxide Hydrolase Conformational Heterogeneity for the Resolution of Bulky Pharmacologically Relevant Epoxide Substrates. Serrano-Hervás E, Casadevall G, Garcia-Borràs M, Feixas F, Osuna S. Chemistry 24 12254-12258 (2018)
  33. Lipase-catalyzed asymmetric synthesis of oxathiazinanones through dynamic covalent kinetic resolution. Hu L, Zhang Y, Ramström O. Org Biomol Chem 12 3572-3575 (2014)
  34. Mini-ISES identifies promising carbafructopyranose-based salens for asymmetric catalysis: Tuning ligand shape via the anomeric effect. Karukurichi KR, Fei X, Swyka RA, Broussy S, Shen W, Dey S, Roy SK, Berkowitz DB. Sci Adv 1 e1500066 (2015)
  35. Directed evolution of mandelate racemase by a novel high-throughput screening method. Yang C, Ye L, Gu J, Yang X, Li A, Yu H. Appl Microbiol Biotechnol 101 1063-1072 (2017)
  36. Engineering the Enantioselectivity and Thermostability of a (+)-γ-Lactamase from Microbacterium hydrocarbonoxydans for Kinetic Resolution of Vince Lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one). Gao S, Zhu S, Huang R, Li H, Wang H, Zheng G. Appl Environ Microbiol 84 e01780-17 (2018)
  37. Significant improvement in catalytic activity and enantioselectivity of a Phaseolus vulgaris epoxide hydrolase, PvEH3, towards ortho-cresyl glycidyl ether based on the semi-rational design. Zhang C, Liu Y, Li C, Xu Y, Su Y, Li J, Zhao J, Wu M. Sci Rep 10 1680 (2020)
  38. Biotransformation of 1,3-propanediol cyclic sulfate and its derivatives to diols by toluene-permeabilized cells of Bacillus sp. CCZU11-1. He YC, Liu F, Zhang DP, Gao S, Li ZQ, Tao ZC, Ma CL. Appl Biochem Biotechnol 175 2647-2658 (2015)
  39. Evaluating Ylehd, a recombinant epoxide hydrolase from Yarrowia lipolytica as a potential biocatalyst for the resolution of benzyl glycidyl ether. Bendigiri C, Harini K, Yenkar S, Zinjarde S, Sowdhamini R, RaviKumar A. RSC Adv 8 12918-12926 (2018)
  40. Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein. Lim H, Jeon HN, Lim S, Jang Y, Kim T, Cho H, Pan JG, No KT. Comput Struct Biotechnol J 20 788-798 (2022)
  41. Homology modelling and site-directed mutagenesis studies of the epoxide hydrolase from Phanerochaete chrysosporium. Zhang LF, Wu JM, Feng H. J Biochem 149 673-684 (2011)
  42. Structural insights into human microsomal epoxide hydrolase by combined homology modeling, molecular dynamics simulations, and molecular docking calculations. Saenz-Méndez P, Katz A, Pérez-Kempner ML, Ventura ON, Vázquez M. Proteins 85 720-730 (2017)
  43. Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network. Mitusińska K, Wojsa P, Bzówka M, Raczyńska A, Bagrowska W, Samol A, Kapica P, Góra A. Comput Struct Biotechnol J 20 193-205 (2022)
  44. The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions. Reetz MT, Garcia-Borràs M. J Am Chem Soc 143 14939-14950 (2021)
  45. Enantioselective Hydrolysis of Styrene Oxide and Benzyl Glycidyl Ether by a Variant of Epoxide Hydrolase from Agromyces mediolanus. Jin H, Li Y, Zhang Q, Lin S, Yang Z, Ding G. Mar Drugs 17 E367 (2019)
  46. Near-perfect kinetic resolution of o-methylphenyl glycidyl ether by RpEH, a novel epoxide hydrolase from Rhodotorula paludigena JNU001 with high stereoselectivity. Xu XF, Hu D, Hu BC, Li C, Liu YY, Wu MC. Appl Microbiol Biotechnol 104 6199-6210 (2020)
  47. Efficient resolution of 3-aryloxy-1,2-propanediols using CLEA-YCJ01 with high enantioselectivity. Wang B, Wu B, He B. RSC Adv 9 13757-13764 (2019)
  48. Enhancement in the catalytic activity of Sulfolobus solfataricus P2 (+)-γ-lactamase by semi-rational design with the aid of a newly established high-throughput screening method. Gao S, Lu Y, Li Y, Huang R, Zheng G. Appl Microbiol Biotechnol 103 251-263 (2019)


Related citations provided by authors (1)

  1. Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases.. Zou J, Hallberg BM, Bergfors T, Oesch F, Arand M, Mowbray SL, Jones TA Structure 8 111-22 (2000)

Quick links