Biochemical nomenclature

Diphosphate, pyrophosphate

Where two phosphoric residues are linked by oxygen atoms, the term "diphosphate" is recommended, rather than pyrophosphate, as in "adenosine diphosphate". Note that "diphosphate" should not be used when two independent phosphoric residues are substituted on different oxygen atoms in a single compound. In this case, the appropriate prefix is "bis", as in "fructose 1,6-bis(phosphate)".

By extension of this principle, for example, the enzyme name "prenyl-diphosphatase" replaces "prenyl-pyrophosphatase".

Thiamin(e)

"Thiamine" and "thiamin" are both used in the literature for vitamin B1. Consultation of the original documents indicated that the first proposal in favour of "thiamine" was accepted in 1951, and that the majority of recommendations since then have been for this form. "Thiamine" is also the International Nonproprietary Name (INN) and therefore has been adopted officially in most countries. "Thiamine" is now used in NC-IUBMB recommendations, and in the Enzyme List. Consequently, the name of the coenzyme is "thiamine diphosphate".

Formimino- an ambiguous term

In the recommendations on folic acid [6], the HN=CH— group, which can be carried on tetrahydrofolate, is called formimino although it is stated that the systematic name is either iminomethyl or formimidoyl. As a result 'formimino' was used in naming enzymes that act on compounds that contain this group. In the naming of the enzymes of histidine biosynthesis, however, the group NH2CH=N-, normally substituted, was called aminoformimino in the reaction of EC 3.5.4.19, phosphoribosyl-AMP cyclohydrolase. This implied that CH2=NH— was called formimino. Because of the confusion between these usages, the Nomenclature Committee has now standardized on the following names:

HN=CH-formimidoyl
CH2=N-methylideneamino
NH2-CH=N-aminomethylideneamino
We encourage the use of these names to avoid ambiguity. This change has led to the amendment of the descriptions of some enzymes in the Enzyme List. The previously used names are added to the list of other name(s).

hydroxy/hydroxyl

Hydroxyl and carboxyl are the only two groups where the name of the group is not the same as the prefix name. Following IUPAC recommendations, it was agreed to use the term with an 'l' at the end (i.e., hydroxyl and carboxyl) only for the radical (see Glossary of class names of organic compounds and reactive intermediates based on structure (IUPAC Recommendations 1994)). This will necessitate amendments to the enzyme list from hydroxyl to hydroxy, e.g., in the case of EC 2.7.1.78 (polynucleotide 5'-hydroxyl-kinase). However hydroxylamine will remain.

NAD or NAD+

Earlier nomenclature documents had offered two alternative ways of describing the reduction of the pyridine nucleotides:

NAD(P)+ + 2 [H] = NAD(P)H + H+

NAD(P) + 2 [H] = NAD(P)H2

The recommendations on the use of "biochemical equations" (see Newsletter 1996) concluded that H+ should be omitted, and hence the form NAD(P)/NAD(P)H2 should be used. However, when it was applied in the Enzyme List, it was criticized by biochemists, on the basis that the information about charge was necessary to understand the mechanism. In view of this, it was decided that, although the various descriptions are all valid, the charged version, i.e., NAD(P)+/NAD(P)H + H+ will be reinstated in the Enzyme List.

A or B, Si or Re specificity for NAD+ and NADP+

Unless one is familiar with the earlier literature on the chirality of NAD(P)+, a name or comment saying that an enzyme is 'A-specific' or 'B-specific' for the nicotinamide ring may hold little meaning. It is recommended that 'A-specific' and 'B-specific' be explained in the comments by the phrases 'is specific for the A (Re)-face of NAD(P)+' and 'is specific for the B (Si)-face of NAD(P)+', respectively.

Oxidized glutathione and other disulfides

Glutathione is g-glutamylcysteinylglycine. When it is oxidized by enzymes or when it acts as a cellular antioxidant, two molecules are linked to form a disulfide (S,S'-biglutathione, abbreviated GSSG). This is commonly described as "oxidized glutathione", but the term is ambiguous, since various other oxidized forms occur in cells, such as the sulfonate. The term now recommended and used in the Enzyme List is 'glutathione disulfide'. This is consistent with the use of the term "disulfide bond" in polypeptide structure.

A number of proteins, such as thioredoxin, contain redox-active cysteine residues that are involved in enzyme reactions. The oxidized forms of these proteins contain an internal disulfide. It was recommended that these are described as disulfides, for example "thioredoxin disulfide".

Selenomethionine

As reported in the 1999 Newsletter, the three-letter code "Sec" and the single-letter code "U" were approved for the rare protein amino-acid selenocysteine. The synthetic amino-acid selenomethionine is introduced into proteins as an isomorphous replacement in crystallographic structure determinations. In order to denote this amino-acid in the structures of proteins, "Sem" was approved as the three-letter code for selenomethionine.

Neoglycoproteins

This term is used for a class of glycoproteins that are formed by covalent attachment of carbohydrate to carbohydrate-free proteins or to glycoproteins by linkages other than glycosyl. Most neoglycoproteins have carbohydrate-protein linkages that do not occur in natural glycoproteins. Examples of substituents (where R is a mono- or oligoglycosyl group) are:

(1)R-O-C6H4-N=N-, where the linkage is to an aryl group in the protein
(2)R-O-CH2-[CHOH]n-CH2-
(3)R-O-CH2-[CH2]n-CO-
(4)HO-CH2-[CHOH]n-CO-CH2-

Substituents (2)-(4) are usually attached to amino groups, N-6 of a lysine residue or N-2 of the N-terminal residue. Example (4) is a glycated protein (see below) and the substituent is often a 1-deoxyfructos-1-yl group.

Glycated proteins

The term glycosylation implies the addition of a glycosyl group. It therefore does not describe the product of the Amadori rearrangement of an N-glycosyl protein, such as occurs naturally by reaction of hemoglobin with blood glucose, giving a N-(1-deoxyfructos-1-yl)hemoglobin, also known as hemoglobin A1c. We recommend that these derivatives be called glycated proteins (this is a narrower definition of the term than that originally proposed in the 1984 Newsletter). This proposal replaces paragraph 5 of the introduction of Nomenclature of glycoproteins, glycopeptides and peptidoglycans (Recommendations 1985). Glycated proteins are thus a subclass of neoglycoproteins.

Reference

6. Biochemical Nomenclature and Related Documents, 2nd edition, 1992, edited by C. Liébecq pp. 266-268, Portland Press, London.


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