How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016)
How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016)
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DOI：
10.1515/pac-2016-0202
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发表时间：
2017-05-01
影响因子：
1.8
通讯作者：
Wittinghofer, Alfred
中科院分区：
文献类型：
--
作者：
Blackburn, G. Michael;Cherfils, Jacqueline;Wittinghofer, Alfred
程序提出了命名的个别原子，P，O，F，N，和S在磷酸酯，酰胺，硫代磷酸酯，多磷酸盐，它们的模拟物，和类似物的过渡态酶催化磷酰基转移反应。其目的是使生物化学、生物物理学、化学、计算化学、晶体学和分子生物学等不同领域的科学家能够共享复杂分子中单个原子的标记标准协议。这将有助于结构结果的清晰和明确的描述，以及有关它们的科学相互交流。目前，仔细阅读蛋白质数据库（PDB）和其他来源表明，在命名上有有限程度的共同性，但在更复杂的结构中有很大程度的不规则性。这里所描述的建议尽可能地遵循既定的实践，特别是IUPAC和IUBMB的建议和PDB中的“最佳实践”，特别是氨基酸的原子标记，特别是立体化学命名的Cahn-Ingold-Prelog规则。它们被设计为在复杂的酶位点中工作以结合磷酸盐，但也可用于非酶系统。最重要的是，这些建议的目的是易于理解和方便用户。
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 enzymecatalyzed 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.