The Enzyme Database


Enzyme Nomenclature News

June 2018

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

[Prepared by Gerry Moss]

The Protein Databank (PDB) includes many examples of phosphoryl transferase enzymes (EC 2.7) that contain phosphates or polyphosphates and their derivatives or mimics. A new IUPAC Recommendation published in Pure and Applied Chemistry* recommends how to identify and uniquely identify each atom of the phosphate or polyphosphate.

For monoesters the phosphorus atoms are identified as PA, PB, PG, PD, etc., starting from the ester end. For diesters the new recommendations explain how to determine which ester should be used to number the phosphorus atoms. When both a nucleic acid and a non-nucleic acid groups are present, the former takes precedence. If both are nucleic acid groups, then alphabetic order (A > C > G > T > U) is used.

With phosphate multi-esters, the phosphorus atoms are identified by the position at which they are attached. For example, in fructose 1,6-bisphosphate the two phosphorus atoms are named P1 and P6. In polyphosphates the phosphorus atoms are named PA1, PB1, PG1, etc.

The oxygen atom directly bonded to the sugar moiety is numbered using the number of the carbon it is attached to. For example, in ATP it is O5′. The other three oxygen atoms of PA are named O1A, O2A and O3A, where O3A bonds to PB, O1A is pro-R, and O2A is pro-S.

When a terminal phosphoryl oxygen is replaced by sulfur, fluorine or nitrogen, the remaining two oxygen atoms are prochiral and are identified accordingly. For example, for ATP with a sulfur substitution, the sulfur atom is named S1G and the two oxygens are O2G (pro-R) and O3G (pro-S).

Where the oxygen is hydrogen bonded to an adjacent amino acid (with bond length 3 Å), the primary sequence number of the amino acid is used to determine the oxygen numbering, as in O1A, O2A, O3A, etc.

Other topics discussed in this recommendation include substitution by other atoms, trigonal bipyramidal phosphate transition state analogues, and metal coordination.

*Pure Applied Chem. 2017, 89(5), 653–675 DOI 10.1515/pac-2016-0202.