How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016)
Year: 2017
Type: article
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.
Source: Pure and Applied Chemistry
Institutions: University of Sheffield, École Normale Supérieure Paris-Saclay, Centre National de la Recherche Scientifique, Laboratoire de Biologie et Pharmacologie Appliquée, Queen Mary University of London, Indiana University – Purdue University Indianapolis, Cardiff University, University of Manchester, Max Planck Institute of Molecular Physiology
Language: English
Subfield: Organic Chemistry
Field: Chemistry
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $2,712
Awards: The influence of metal fluorides on the structure and dynamics of phosphoryl transfer enzymes, Dynamics, Gating and Opening in Enzyme Catalysis, Understanding enzyme-catalysed phosphoryl transfer, Enzyme catalysis of nucleophilic attack of anions by anions, Residue-specific contributions to the energetics of the catalytic cycle of PGK
OpenAlex ID: W2610426681