ArticleJournal of molecular biology2022
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.
Article in Journal of molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 51 citations in OpenAlex.
- Article
- Proteome-Wide Target Identification Using Reactive Metallo-Scaffolds (r-mS): A Platform for Metallodrug Discovery.Angewandte Chemie (International ed. in English) · 2026Article
- Investigating enzyme function by geometric matching of catalytic motifs.Protein science : a publication of the Protein Society · 2026Article
- MutexaGPT: An Intuition-to-Design Translator for Physics-based Enzyme Engineering.Research square · 2026Article
- Discovery of a potent covalent inhibitor that unusually distorts the catalytic dyad of SARS-CoV-2 main protease.Journal of virology · 2025Article
- SubTuner leverages physics-based modeling to complement AI in enzyme engineering toward non-native substrates.Chem catalysis · 2025Article
- Replicating PET Hydrolytic Activity by Positioning Active Sites with Smaller Synthetic Protein Scaffolds.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.Nucleic acids research · 2025Article
- Paradigms of convergent evolution in enzymes.The FEBS journal · 2025Article
- A role for conformational changes in enzyme catalysis.Biophysical journal · 2024Article
- Sequence-Structure Analysis Unlocking the Potential Functional Application of the Local 3D Motifs of Plant-Derived Diterpene Synthases.Biomolecules · 2024Article
- Virtual screening and molecular dynamics studies of novel small molecules targetingIn silico pharmacology · 2024Article
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- A Proofreading Mutation with an Allosteric Effect Allows a Cluster of SARS-CoV-2 Viruses to Rapidly Evolve.Molecular biology and evolution · 2023Article
- Catalytic site flexibility facilitates the substrate and catalytic promiscuity of Vibrio dual lipase/transferase.Nature communications · 2023Article
- AlphaFold2 protein structure prediction: Implications for drug discovery.Current opinion in structural biology · 2023Review
- Influence of the Active Site Flexibility on the Efficiency of Substrate Activation in the Active Sites of Bi-Zinc Metallo-β-Lactamases.Molecules (Basel, Switzerland) · 2022Article
- Capturing the geometry, function, and evolution of enzymes with 3D templates.Protein science : a publication of the Protein Society · 2022Review
- A review on application of molecular simulation technology in food molecules interaction.Current research in food science · 2022Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Conformational variation in catalytic residues can be captured as alternative snapshots in enzyme crystal structures. Addressing the question of whether active site flexibility is an intrinsic and essential property of enzymes for catalysis, we present a comprehensive study on the 3D variation of active sites of 925 enzyme families, using explicit catalytic residue annotations from the Mechanism and Catalytic Site Atlas and structural data from the Protein Data Bank. Through weighted pairwise superposition of the functional atoms of active sites, we captured structural variability at single-residue level and examined the geometrical changes as ligands bind or as mutations occur. We demonstrate that catalytic centres of enzymes can be inherently rigid or flexible to various degrees according to the function they perform, and structural variability most often involves a subset of the catalytic residues, usually those not directly involved in the formation or cleavage of bonds. Moreover, data suggest that 2/3 of active sites are flexible, and in half of those, flexibility is only observed in the side chain. The goal of this work is to characterise our current knowledge of the extent of flexibility at the heart of catalysis and ultimately place our findings in the context of the evolution of catalysis as enzymes evolve new functions and bind different substrates.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.