ArticleBiochemistry2011
Evidence of the participation of remote residues in the catalytic activity of Co-type nitrile hydratase from Pseudomonas putida.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 52 citations in OpenAlex.
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- Biochemical Characterization of Disease-Associated Variants of Human Ornithine Transcarbamylase.ACS chemical biology · 2025Article
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- Electrostatic fingerprints of catalytically active amino acids in enzymes.Protein science : a publication of the Protein Society · 2022Article
- Second-Shell Amino Acid R266 Helps DetermineBiochemistry · 2021Article
- Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase.Protein science : a publication of the Protein Society · 2021Article
- Biodegradation of flonicamid by Ensifer adhaerens CGMCC 6315 and enzymatic characterization of the nitrile hydratases involved.Microbial cell factories · 2021Article
- A low CO2-responsive mutant of Setaria viridis reveals that reduced carbonic anhydrase limits C4 photosynthesis.Journal of experimental botany · 2021Article
- Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase.PloS one · 2020Article
- Advances in cloning, structural and bioremediation aspects of nitrile hydratases.Molecular biology reports · 2019Review
- Probing the Effect of Glucose on the Activity and Stability of β-Glucosidase: An All-Atom Molecular Dynamics Simulation Investigation.ACS omega · 2019Article
- The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths.PLoS computational biology · 2017Article
- Analyzing the catalytic role of active site residues in the Fe-type nitrile hydratase from Comamonas testosteroni Ni1.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- Prediction of distal residue participation in enzyme catalysis.Protein science : a publication of the Protein Society · 2015Article
- The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile.Journal of the American Chemical Society · 2014Article
- Article
- POOL server: machine learning application for functional site prediction in proteins.Bioinformatics (Oxford, England) · 2012Article
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues (α-Asp164, β-Glu56, and β-His147) and one predicted third-shell residue (β-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues (α-Glu168) and the three residues not predicted (α-Arg170, α-Tyr171, and β-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.
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