ArticleScientific reports2014
How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- It started off as a Cys, how did it end up like this? Identifying the extent of unmodelled oxidatively modified cysteines within the Protein Data Bank.Acta crystallographica. Section D, Structural biology · 2026Article
- The Essential Role of Water Molecules in the Reaction Mechanism of Protein O-Fucosyltransferase 2.Angewandte Chemie (International ed. in English) · 2022Article
- Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria.Nucleic acids research · 2022Article
- Guanidine- and purine-functionalized ligands of FeJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2019Article
- Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition.PloS one · 2017Article
- Zinc(II) Binding Site to the Amyloid-β Peptide: Insights from Spectroscopic Studies with a Wide Series of Modified Peptides.Inorganic chemistry · 2016Article
- Synchrotron X-ray footprinting as a method to visualize water in proteins.Journal of synchrotron radiation · 2016Article
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Authors and funding
11 authors.
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Abstract
Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.
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