How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016)

G Michael Blackburn, Jacqueline Cherfils, Gerard P. Moss, Nigel G. J. Richards, Jonathan P. Waltho, Nicholas H. Williams, Alfred Wittinghofer

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    Abstract

    Procedures are proposed for the naming of individual atoms, P, O, F, N, and S in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalyzed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g. biochemistry, biophysics, chemistry, computational chemistry, crystallography, and molecular biology, to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results, as well as scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature, but a large measure of irregularity in more complex structures. The recommendations described here adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations and to "best practice" in the PDB, especially to its atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be easy to comprehend and user-friendly.

    Original languageEnglish
    Pages (from-to)653-675
    Number of pages23
    JournalPure and Applied Chemistry
    Volume89
    Issue number5
    Early online date29 Apr 2017
    DOIs
    Publication statusPublished - 1 May 2017

    Keywords

    • atom names for transition states
    • naming phosphate transition states
    • P, O, F and N atom labels
    • phosphate analogues
    • phosphate atom labels
    • phosphate nomenclature
    • phosphate stereochemical naming
    • phosphoryl transfer
    • polyphosphates
    • recommendations

    Research Beacons, Institutes and Platforms

    • Manchester Institute of Biotechnology

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