5YNG
Crystal structure of SZ348 in complex with cyclopentene oxide
Summary for 5YNG
| Entry DOI | 10.2210/pdb5yng/pdb |
| Descriptor | Limonene-1,2-epoxide hydrolase, POTASSIUM ION, NICKEL (II) ION, ... (5 entities in total) |
| Functional Keywords | epoxide hydrolase, cyclopentene oxide, hydrolase |
| Biological source | Rhodococcus erythropolis (Arthrobacter picolinophilus) |
| Total number of polymer chains | 2 |
| Total formula weight | 35134.66 |
| Authors | Wu, L.,Sun, Z.T.,Reetz, M.T.,Zhou, J.H. (deposition date: 2017-10-24, release date: 2018-06-27, Last modification date: 2024-03-27) |
| Primary citation | Sun, Z.,Wu, L.,Bocola, M.,Chan, H.C.S.,Lonsdale, R.,Kong, X.D.,Yuan, S.,Zhou, J.,Reetz, M.T. Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations. J. Am. Chem. Soc., 140:310-318, 2018 Cited by PubMed Abstract: Directed evolution of limonene epoxide hydrolase (LEH), which catalyzes the hydrolytic desymmetrization reactions of cyclopentene oxide and cyclohexene oxide, results in (R,R)- and (S,S)-selective mutants. Their crystal structures combined with extensive theoretical computations shed light on the mechanistic intricacies of this widely used enzyme. From the computed activation energies of various pathways, we discover the underlying stereochemistry for favorable reactions. Surprisingly, some of the most enantioselective mutants that rapidly convert cyclohexene oxide do not catalyze the analogous transformation of the structurally similar cyclopentene oxide, as shown by additional X-ray structures of the variants harboring this slightly smaller substrate. We explain this puzzling observation on the basis of computational calculations which reveal a disrupted alignment between nucleophilic water and cyclopentene oxide due to the pronounced flexibility of the binding pocket. In contrast, in the stereoselective reactions of cyclohexene oxide, reactive conformations are easily reached. The unique combination of structural and computational data allows insight into mechanistic details of this epoxide hydrolase and provides guidance for future protein engineering in reactions of structurally different substrates. PubMed: 29232125DOI: 10.1021/jacs.7b10278 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.497 Å) |
Structure validation
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