ArticleProtein science : a publication of the Protein Society2019
Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes.
Article in Protein science : a publication of the Protein Society, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- A Sequence-Based Approach Reveals a Novel Family IV Lipolytic Enzyme in Cereibacter sphaeroides 2.4.1.Molecular biotechnology · 2026Article
- Catalytic His-loop flexibility drives high activity in hyperthermophilic esterase EstE1 while preserving structural stability.Microbiology spectrum · 2025Article
- The reaction mechanism for glycolysis side product degradation by Parkinson's disease-linked DJ-1.The Journal of cell biology · 2025Article
- α/β Hydrolases: Toward Unraveling Entangled Classification.Proteins · 2025Article
- Structural Catalytic Core in Subtilisin-like Proteins and Its Comparison to Trypsin-like Serine Proteases and Alpha/Beta-Hydrolases.International journal of molecular sciences · 2024Review
- Structural insights into strigolactone catabolism by carboxylesterases reveal a conserved conformational regulation.Nature communications · 2024Article
- Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance.Journal of molecular biology · 2024Article
- Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone.ACS catalysis · 2024Article
- The active site of the SGNH hydrolase-like fold proteins: Nucleophile-oxyanion (Nuc-Oxy) and Acid-Base zones.Current research in structural biology · 2024Article
- Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the α/β-hydrolase fold.Chemical science · 2023Article
- Microbiological Characterization of the Biofilms Colonizing Bioplastics in Natural Marine Conditions: A Comparison between PHBV and PLA.Microorganisms · 2023Article
- Knotting terminal ends of mutant T1 lipase with disulfide bond improved structure rigidity and stability.Applied microbiology and biotechnology · 2023Article
- Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion.Nature communications · 2022Article
- Thermostable lipases and their dynamics of improved enzymatic properties.Applied microbiology and biotechnology · 2021Review
- Conformational gating, dynamics and allostery in human monoacylglycerol lipase.Scientific reports · 2020Article
- Structural insights into the putative bacterial acetylcholinesterase ChoE and its substrate inhibition mechanism.The Journal of biological chemistry · 2020Article
- NBCZone: Universal three-dimensional construction of eleven amino acids near the catalytic nucleophile and base in the superfamily of (chymo)trypsin-like serine fold proteases.International journal of biological macromolecules · 2020Article
- The structural basis of fungal glucuronoyl esterase activity on natural substrates.Nature communications · 2020Article
- The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements.PloS one · 2020Article
- Distinct roles of an ionic interaction holding an alpha-helix with catalytic Asp and a beta-strand with catalytic His in a hyperthermophilic esterase EstE1 and a mesophilic esterase rPPE.Extremophiles : life under extreme conditions · 2019Article
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Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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