Elucidation of the Catalytic Mechanism of a Miniature Zinc Finger Hydrolase
| Autor: | David Möller, Elsa Sanchez-Garcia, Trung Quan Luong, Frank Schulz, Roland Winter, Simon Ebbinghaus, Abir Ganguly, Walter Thiel, Michael Dirkmann, Oliver Brylski |
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| Rok vydání: | 2017 |
| Předmět: |
Hydrolases
Stereochemistry Chemie Molecular Conformation chemistry.chemical_element Zinc Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Catalysis chemistry.chemical_compound Molecular dynamics Nucleophile Tetrahedral carbonyl addition compound Carbonic anhydrase 0103 physical sciences Hydrolase Materials Chemistry Organic chemistry Physical and Theoretical Chemistry 010304 chemical physics biology Chemistry Water Zinc Fingers 0104 chemical sciences Surfaces Coatings and Films Kinetics Biocatalysis biology.protein Quantum Theory Hydroxide |
| Zdroj: | The Journal of Physical Chemistry B. 121:6390-6398 |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/acs.jpcb.7b05027 |
| Popis: | To improve our mechanistic understanding of zinc metalloenzymes, we report a joint computational and experimental study of a minimal carbonic anhydrase (CA) mimic, a 22-residue Zn-finger hydrolase. We combine classical molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) geometry optimizations, and QM/MM free energy simulations with ambient and high-pressure kinetic measurements to investigate the mechanism of the hydrolysis of the substrate p-nitrophenylacetate (pNPA). The zinc center of the hydrolase prefers a pentacoordinated geometry, as found in most naturally occurring CAs and CA-like enzymes. Two possible mechanisms for the catalytic reaction are investigated. The first one is analogous to the commonly accepted mechanism for CA-like enzymes: a sequential pathway, in which a Zn2+-bound hydroxide acts as a nucleophile and the hydrolysis proceeds through a tetrahedral intermediate. The initial rate-limiting step of this reaction is the nucleophilic attack of the hydroxide... |
| Databáze: | OpenAIRE |
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