Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
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To efficiently catalyze a chemical reaction, enzymes are required to maintain fast rates for formation of the Michaelis complex, the chemical reaction and product release. These distinct demands could be satisfied via fluctuation between different conformational substates (CSs) with unique configurations and catalytic properties. However, there is debate as to how these rapid conformational changes, or dynamics, exactly affect catalysis. As a model system, we have studied bacterial phosphotriesterase (PTE), which catalyzes the hydrolysis of the pesticide paraoxon at rates limited by a physical barrier—either substrate diffusion or conformational change. The mechanism of paraoxon hydrolysis is understood in detail and is based on a single, dominant, enzyme conformation. However, the other aspects of substrate turnover (substrate binding and product release), although possibly rate-limiting, have received relatively little attention. This work identifies “open” and “closed” CSs in PTE and dominant structural transition in the enzyme that links them. The closed state is optimally preorganized for paraoxon hydrolysis, but seems to block access to/from the active site. In contrast, the open CS enables access to the active site but is poorly organized for hydrolysis. Analysis of the structural and kinetic effects of mutations distant from the active site suggests that remote mutations affect the turnover rate by altering the conformational landscape.
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For bacterial phosphotriesterase, maltose binding protein, choline oxidase, cytochrome bc1 complex, and many lid-gated enzymes, closed and open conformations are in equilibrium prior to ligand binding, permitting conformational selection at different catalytic steps.
“Conformational sampling for bacterial phosphotriesterase,443 maltose binding protein,444 and choline oxidase,445 cytochrome bc1 complex,446 and many other lid-gated enzymes indicated that the closed and open conformations are in equilibrium prior to ligand binding, permitting a conformational selection pathway at different catalytic steps.447”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [443]
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(2019) · Biointerface Research in Applied Chemistry · doi:10.33263/briac91.817824 · Cited by 24 · see citing works
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X-ray crystallography at the heart of life science
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Mutation of outer-shell residues modulates metal ion co-ordination strength in a metalloenzyme
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Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity
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The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes*
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Enzyme Dynamics and Engineering: One Step at a Time
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Experimental and In Silico Analysis of TEM β-Lactamase Adaptive Evolution
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Adventures on the Routes of Protein Evolution—In Memoriam Dan Salah Tawfik (1955–2021)
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Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function
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Computational Design of Phosphotriesterase Improves V‐Agent Degradation Efficiency
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Design and Evolution of Artificial Metalloenzymes: Biomimetic Aspects
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- Authors
- Jackson, C. J., Foo, J.-L., Tokuriki, N., Afriat, L., Carr, P. D., Kim, H.-K., Schenk, G., Tawfik, D. S., & Ollis, D. L.
- Affiliations
- Institut de Biologie Structurale (FR)
- Australian National University (AU)
- University of Cambridge (GB)
- Weizmann Institute of Science, Rehovot 76100, Israel;
- The University of Queensland (AU)
- Weizmann Institute of Science (IL)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2009-12-22
- Volume
- 106
- Issue
- 51
- Pages
- 21631-21636
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2799856
- OpenAlex
- W2000385523
- Cited by
- 119
- References
- 45
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 9 · 2023: 5 · 2022: 7 · 2021: 2 · 2020: 4 · 2019: 8 · 2018: 5 · 2017: 8 · 2016: 11 · 2015: 12 · 2014: 7 · 2013: 9 · 2012: 7
- FWCI
- 3.62
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Reaction Mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- conformational states, enzyme catalysis, paraoxon hydrolysis, enzyme dynamics, conformational change, substrate binding, product launch, active site access, conformational landscape, enzyme evolution, pesticide hydrolysis
- MeSH terms
- Bacteria, Kinetics, Models, Molecular, Mutation, Protein Conformation, Evolution, Molecular, Phosphoric Triester Hydrolases, Biocatalysis
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