Biochemical Nomenclature Committee of IUPAC and NC-IUBMB

Newsletter 2018

May be freely published and quoted by journals

Ribonuclease classification

[Prepared by Keith Tipton]

The classification of the ribonucleases has been a matter of some contention. Whereas some appear to act as simple hydrolases, cleaving the 3',5'-phosphatodiester bonds linking adjacent nucleotides, others, such as pancreatic ribonuclease, cleave to give a 2',3'-cyclophosphate derivative, which is subsequently hydrolysed to the 3'-phosphate, as shown below.

Pancreatic ribonuclease was listed among those enzymes transferring phosphate groups, Enzymes catalysing other phosphate-transfer reactions, as entry 502 in the Table of Enzymes published by Dixon & Webb in 1958 [1]. When the Enzyme List was formally divided into specific reaction classes, it was listed as a transferase, (EC 2.7.7.16) in 1961 [2], but, since the overall reaction was hydrolysis, it was reclassified as a hydrolase (EC 3.1.27.5) in 1972 [3]. However, it became clear that neither of these classification types adequately described the activity of this enzyme. The cyclophosphate produced in reaction I is actually released from the enzyme and the subsequent hydrolytic step (reaction II), which occurs by a reversal of reaction I with the hydroxyl group of water replacing the 5'-hydroxyl group of ribose, only occurring to any appreciable extent when the formation of the cyclophosphate product is essentially complete. Thus the reaction may be regarded as that of a lyase (a phosphorous-oxygen lyase) since it 'cleaves bonds by means other than by hydrolysis or oxidation'. This is the class of enzyme where two (or more) substrates are involved in one reaction direction, but there is one compound fewer in the other direction and when acting on the single substrate, a molecule is eliminated and this generates either a new double bond or, in this case, a new ring structure.

Because of this, pancreatic ribonuclease and some other ribonucleases have now been reclassified as phosphorous-oxygen lyases (EC 4.6.1.-). Those ribonucleases which appear to behave as simple hydrolases remain in EC 3 along with the DNases, which cannot form 2',3'-cyclophosphate products.

1. Dixon M. & Webb EC. (1958) Enzymes, Longmans Green, London, pp. 185-227.

2. Report of the Commission on Enzymes of the International Union of Biochemistry (1961). Pergamon Press, New York & London.

3. Enzyme Nomenclature (1973) Recommendations (1972) of the Commission on Biochemical Nomenclature on the Nomenclature and Classification of Enzymes, Together with their Units and the Symbols of Enzyme Kinetics. Elsevier, Amsterdam.

Translocases (EC 7): A new EC Class

[Prepared by Keith Tipton]

Six enzyme classes have been recognized since the first Enzyme classification and nomenclature list was first approved by the International Union of Biochemistry in 1961. These were based on the type of reaction catalysed: Oxidoreductases (EC 1), Transferases (EC 2), Hydrolases (EC 3), Lyases (EC 4), Isomerases (EC 5) and Ligases (EC 6). However, it has become apparent that none of these could describe the important group of enzymes that catalyse the movement of ions or molecules across membranes or their separation within membranes. Several of these involve the hydrolysis of ATP and had been previously classified as ATPases (EC 3.6.3.-), although the hydrolytic reaction is not their primary function.

These enzymes have now been classified under a new EC class of translocases (EC 7).The reactions catalysed are designated as transfers from ‘side 1’ to ‘side 2’ because the designations ‘in’ and ‘out’ (or ‘cis’ and ‘trans’), which had been used previously, lack clarity and can be ambiguous. The comments associated with each entry then describe the specific translocations catalysed.

The subclasses designate the types of ion or molecule translocated:
EC 7.1 contains enzymes catalysing the translocation of hydrons (hydron being the general name for H⁺ in its natural abundance),
EC 7.2 contains those catalysing the translocation of inorganic cations and their chelates,
EC 7.3 contains those catalysing the translocation of inorganic anions,
EC 7.4 contains those catalysing the translocation of amino acids and peptides,
EC 7.5 contains those catalysing the translocation of carbohydrates and their derivatives
EC 7.6 contains those catalysing the translocation of other compounds.

The sub-subclasses concern the reaction that provided the driving force for the translocation, where these are relevant:
EC 7.x.1 translocations linked to oxidoreductase reactions
EC 7.x.2 translocations linked to the hydrolysis of a nucleoside triphosphate
EC 7.x.3 translocations linked to the hydrolysis of a diphosphate
EC 7.x.4 translocations linked to a decarboxylation reaction
Exchange transporters that are not dependent on enzyme-catalysed reactions, such as the exchange of ions across membranes, are not included and pores that change conformation between open and closed states in response to phosphorylation or some other catalysed reaction are classified under EC 5.6 (Macromolecular conformational isomerases).

(We are grateful to Dr Amanda Mackie (Macquarie University) for her advice on the content of this EC class)

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.

Classification of cytochrome P-450 enzymes by the Enzyme Commission

[Prepared by Ron Caspi]

Cytochrome P-450 enzymes (CYPs) are a large family of heme-containing proteins found in all kingdoms of life. The term "P-450" is derived from the spectrophotometric peak at the wavelength of the absorption maximum of the enzyme (450 nm) when it is in the reduced state and complexed with carbon monoxide. More than 50,000 distinct CYP proteins have been described.

The CYPs are classified into several groups, the main ones being eukaryotic microsomal enzymes, eukaryotic mitochondrial enzymes, and bacterial enzymes. While most CYPs require electrons that originate from NADPH, almost no such enzyme can receive the electrons directly from NADPH, and a secondary electron transfer protein is involved. The classification of CYPs by the Enzyme Commission is determined by the type of reaction they catalyse and the type of electron donor with which they interact.

For microsomal enzymes, the usual electron donor is EC 1.6.2.4, NADPH-hemoprotein reductase. When the reaction involves monooxygenation and formation of a single molecule of water, the enzyme should be classified under EC 1.14.14: oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen, with reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor (e.g. EC 1.14.14.16, steroid 21-monooxygenase).

Bacterial CYPs usually utilize ferredoxin. These enzymes are classified under EC 1.14.15: oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen, with reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor (e.g. EC 1.14.15.8, steroid 15β-monooxygenase).

Mitochondrial CYPs utilize a specialized ferredoxin, known as adrenodoxin, as their electron donor, and are thus also classified under EC 1.14.15. (e.g. EC 1.14.15.15, cholestanetriol 26-monooxygenase).

When the reaction involves the formation of two molecules of water, the enzyme should be classified under EC 1.14.19: oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen, with oxidation of a pair of donors resulting in the reduction of O₂ to two molecules of water (e.g. EC 1.14.19.52, camalexin synthase).

Exceptions do occur — for example, CYPs from the CYP74 family catalyse dehydration reactions that do not require oxygen or an electron donor and are classified under EC 4.2.1 (e.g. EC 4.2.1.121, colneleate synthase). A number of CYPs catalyse an isomerization reaction and should be classified under the proper sub-subclass for the particular isomerization reaction (e.g. EC 5.3.99.4, prostaglandin-I synthase). Unfortunately, in the past many CYPs have been misclassified under EC 1.14.13, which should be used for enzymes that use NADH/NADPH as their direct electron source. In the coming months these entries will be reclassified under the proper sub-subclass.