A0710 1.1

Sinead Boyce, Trinity College, Dublin, Ireland Keith F Tipton, Trinity College, Dublin, Ireland Enzyme classification and nomenclature is a system that allows the unambiguous identification of enzymes in terms of the reactions they catalyse. This relies on a numerical system to class enzymes in groups according to the types of reaction catalysed andsystematic naming that describes the chemical reaction involved.
another phosphate-containing group through its phos- The need for a rational nomenclature for enzymes can be phate to another substrate, it is a phosphotransferase seen from the plethora of unhelpful names for enzymes in classified as EC 2.7. z.–, where z refers to the nature of the the earlier literature. Only those who were directly involved acceptor group, and so on. The detailed descriptions of the might have known the difference between the old yellow procedures for assigning enzymes to specific classes and enzyme and the new yellow enzyme and what diaphorase, subclasses and the rules for systematic enzyme names that or for that matter DT-diaphorase, catalysed (try EC have been approved by the IUBMB Nomenclature 1.6.99.1 and EC 1.8.1.4). Similarly, the reaction catalysed Committee have been published in Enzyme Nomenclature by rhodenese (thiosulfate sulfurtransferase: EC 2.8.1.1) (1992). The account below has been adapted from the fuller was not apparent from its name and use of the name material in that source, which should be consulted if urokinase to describe a peptidase (EC 3.4.21.73) is confusing since the term kinase is usually used for enzymesthat transfer phosphate from ATP to another substrate.
In trying to bring some order to the chaotic situation of enzyme nomenclature, Malcolm Dixon and Edwin Webb, in 1958, took a step that was radically different from thatused in other branches of nomenclature by classifying The basic layout of the classification for each enzyme is enzymes in terms of the reactions they catalysed, rather described below with some indication of the guidelines than by their structures. This system has been adopted and followed. Further details of the principles governing the developed by the International Union of Biochemistry and nomenclature of individual enzyme classes are given in the Molecular Biology (IUBMB), through its Joint Nomen- clature Committee with the International Union of Pure The classification number, which is made and Applied Chemistry (IUPAC) into the Enzyme up of four digits, identifies the enzyme by the reaction Nomenclature list of enzymes. This has been through catalysed. This is also valuable for relating the information several editions, the most recent being published in 1992.
This material is also made available in a modified form through the SWISSPROT ENZYME on-line database.
for the enzyme is usually used, provided that it is More recent additions and modifications to the list have unambiguous. A number of generic words indicating been published as supplements in the European Journal of reaction types may be used in recommended names, but Biochemistry and the most recent additions are available not in the systematic names, e.g. dehydrogenase, reductase, on-line (see Enzyme Supplement, 1999 in Further Reading oxidase, peroxidase, kinase, tautomerase, deaminase, dehy- dratase, etc. Where additional information is needed to Detailed rules for naming and classifying enzymes have make the reaction clear, a phrase indicating the reaction or been formulated and it is a relatively easy matter to assign a product may be added in parentheses after the second an enzyme to an overall class and to give it a name that part of the name, e.g. (ADP-forming), (dimerizing), (CoA- describes what it does. For example, if it oxidizes some- thing by reducing NAD(P), it is a dehydrogenase classified as EC 1. x. 1. – , where the number x refers to the group where possible, in the form of a ‘biochemical’ equation [I]: oxidized: 1 for –CHOH–, 2 for aldehyde or ketone, etc.; however, if it transfers a phosphate, diphosphate or ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net This formulation gives no indication of the preferred mitter norepinephrine (noradrenaline) has a systematic equilibrium of the reaction or, indeed, whether it is readily name of (R)-4-(2-amino-1-hydroxyethyl)-1,2-benzenediol, reversible. In the case of reversible reactions, the direction the antibiotic benzylpenicillin is [2S-(2a,5a, 6b)]-3,3- chosen for the reaction and systematic name is the same for dimethyl-7-oxo-6-[(phenylacetyl)amino]-4-thia-1-azabi- all the enzymes in a given class, even if this direction has not cyclo[3.2.0]heptane-2-carboxylic acid and aspirin is 2- been demonstrated for all. Thus, systematic names are based on this written reaction, even though only the reverse The basic rules for writing down the systematic name of of this may actually have been demonstrated experimen- a compound are to take a basic, or root, structure or its tally. Frequently, such biochemical equations are neither derivative, for example benzoic acid is the derivative of the root benzene in the case of aspirin. The substituents are then written before it with the position of each substituent for the enzyme. This is to be as comprehensive a list as and any stereochemistry being identified. There are several possible to aid searching for any specific enzyme. The possible modifications of this procedure and it is possible to inclusion of a name in this list does not mean that its use is write more than one systematic name that is more-or-less encouraged. In some cases where the same name has been unambiguous (see for example, the alternative names that given to more than one enzyme, this ambiguity will be have been used for norepinephrine in the Merck Index).
Variations arise, for example, from the choice of root compound and the order in which the substituents are biguous terms what the enzyme actually catalyses.
written. Where systematic names are used, the enzyme Systematic names consist of two parts. The first contains classification system uses the IUPAC system, which uses the name of the substrate or, in the case of a bimolecular rather few root compounds and writes the substituents in reaction, of the two substrates separated by a colon. The alphabetical order (e.g. amino before hydroxy, before second part, ending in -ase, indicates the nature of methyl etc.). Chemists use fewer root structures than the reaction. A number of generic words indicating a type biochemists. For example, biochemists all know the amino of reaction may be used in either recommended or acid tryptophan and that it can be decarboxylated to systematic names: oxidoreductase, oxygenase, transferase tryptamine. Therefore, they have no trouble with naming (with a prefix indicating the nature of the group the hormone melatonin N-acetyl-5-methoxytryptamine.
transferred), hydrolase, lyase, racemase, epimerase, iso- However, if a chemist does not accept tryptamine as a root merase, mutase, ligase. Where additional information is structure it would become N-[2-(5-methoxy-1H-indol-3- needed to make the reaction clear, a phrase indicating the yl)ethyl]acetamide. Because the enzyme classification reaction or a product should be added in parentheses after system is primarily designed for biochemists, the biochem- the second part of the name, e.g. (ADP-forming), (dimeriz- ical names are frequently used, where these are widely known. However, collaboration with IUPAC ensures that the systematic names can be readily found from these in reaction catalysed, possible relationships to other enzymes, species differences, metal-ion requirement, etc.
It should be noted that the systematic names of Key references on the identification, nat- norepinephrine and melatonin are single ‘words’, which ure, properties and function of the enzyme. These have can contain lots of hyphens in them and generally been omitted from the examples below to save space.
systematic names are written as single ‘words’. Amongthe few exceptions to this general rule are acids, includingphosphates, as shown by the examples of penicillin andaspirin, where ‘acid’ is written as a separate word. Similarly creatine phosphate is written as two words, although it ispossible to write the compound as a single word by Although a detailed description of chemical nomenclature rearranging the name to phosphocreatine. An example of is beyond the scope of this article, some comments are such rearrangement is the name 6-phosphofructokinase necessary because the fearsome names used are often for the enzyme (EC 2.7.1.11) that catalyses the reaction: difficult for a biochemist to understand. The aim of the chemist is to be able to name a compound in such a way that anyone who knows the rules of chemical nomenclaturecan write down its chemical structure and formula from it.
Note that the term bisphosphate is used here rather than Therefore, it must be unambiguous both in terms of all the diphosphate. In order to avoid confusion, diphosphate is chemical groups that make up the compound, how and used only for cases where the two phosphates are linked where they are linked together and the compound’s together (as in adenosine diphosphate; ADP) whereas stereochemistry. This does lead to names that are not bisphosphates have the two phosphates attached to much help for general use, for example, the neurotrans- ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net When a substrate name has two words there is a The second figure in the code number of the oxidor- potential problem using them in enzyme names. Glucose- eductases denotes the type of group in the hydrogen-donor 6-phosphate 1-dehydrogenase (EC 1.1.1.49) catalyses the substrate that is oxidized or reduced. The third number denotes the hydrogen acceptor: 1 denotes NAD(P), 2 acytochrome, 3 molecular oxygen, 4 a disulfide, 5 a quinone d-glucose 6-phosphate 1 NADP = d-glucono-1,5-lac- or similar compound, 6 a nitrogenous group, 7 an iron– sulfur protein and 8 a flavin. The number 99 is used for allother acceptors. This group contains a number of enzymes but in order to indicate that the substrate oxidized is that have been shown to work with synthetic acceptors, glucose 6-phosphate, not just phosphate, an extra hyphen such as 2,6-dichloroindophenol or phenazine methosul- fate, but where the physiological acceptor is unknown. It is In denoting stereochemistry, the IUPAC rules prefer the intended that they should be transferred to more descrip- R- and S- system and this is generally used for enzyme tive sub-subclasses when the natural acceptor is identified.
nomenclature. However, in the case of sugars and amino For subclasses 1.13 and 1.14, a different classification acids, the d- and l- designations are so well known that scheme is used since these enzymes catalyse the incorpora- they are followed in the enzyme list. The use of italics in tion of oxygen into the substrate. The recommended names chemical names can at first seem rather odd, but the are generally monooxygenase or dioxygenase, depending simplest way of thinking about it is to think how one would on whether one or two atoms of oxygen are incorporated look up the name of a compound in an index, for example into the substance oxidized. The sub-subclasses are N-acetyl-5-methoxytryptamine would be found by search- ing through A for acetyl not N for N-acetyl. Clearly the Table 1 summarizes the structure of Class 1.
same applies to R- and S-isomers. Therefore, the italic canbe taken to mean ‘do not bother to look under this letter in any index’. Having adopted this way of doing things, it islogical also to use italics for these when they occur in the middle of a name. The exceptions to this general rule are Recommended name: l-iditol 2-dehydrogenase the d- and l- designations, which are not italicized, Reaction: l-iditol 1 NAD 5 l-sorbose 1 NADH2 however, these are written, by convention, in a smaller The above summary glosses over many of the complex- Systematic name: l-iditol:NAD 2-oxidoreductase ities of systematic chemical nomenclature and fuller details Comments: Also acts on d-glucitol (giving d-fructose) of the rules and their application can be found in A Guide to and other closely related sugar alcohols.
IUPAC Nomenclature of Organic Compounds (1994) .
Reaction:l-lysine 1 NADPH2 1 O2 5 N6-hydroxy-l- Systematic name: l-lysine, NADPH2:oxygen oxidore- This class contains the enzymes catalysing oxidation Comments: A flavoprotein (FAD). The enzyme from reactions. Since the oxidation of one group must be strain EN 222 of E. coli is highly specific for l-lysine; l- accompanied by the reduction of another, they are grouped ornithine and l-homolysine are, for example, not sub- together as oxidoreductases. The systematic enzyme name strates. A lysine monooxygenase (EC 1.13.12.10) from this is in the form donor:acceptor oxidoreductase. The substrate organism has been reported to catalyse the same hydro- that is being oxidized is regarded as being the hydrogen xylation without the involvement of NAD(P)H donor. The recommended name is commonly donor dehydrogenase. Although the term reductase is sometimesused as an alternative, it is important to remember that the recommended name does not define the equilibriumposition of the reaction or the net direction of flux through These enzymes transfer a group from one substrate (the the enzyme in vivo. Indeed, in some cases, an enzyme within donor) to another (the acceptor) according to the general a metabolic pathway can proceed in a thermodynamically unfavoured direction because of the effective removal of one of the reactants. The term donor oxidase is used onlywhen O2 is the acceptor.
ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net Table 1 Class 1.–.–.– Oxidorectuses
1. 1.–.– Acting on the CH–OH group of donors 1. 1. 2.– With a cytochrome as acceptor 1. 1. 5.– With a quinone or similar compound as acceptor 1. 2. –.– Acting on the aldehyde or oxo group of donors 1. 2. 2.– With a cytochrome as acceptor 1. 2. 7.– With an iron–sulfur protein as acceptor 1. 3.–.– Acting on the CH–CH group of donors 1. 3. 2.– With a cytochrome as acceptor 1. 3. 5.– With a quinone or related compound as acceptor 1. 3. 7.– With an iron–sulfur protein as acceptor 1. 4.–.– Acting on the CH–NH2 group of donors 1. 4. 2.– With a cytochrome as acceptor 1. 4. 7.– With an iron–sulfur protein as acceptor 1. 5.–.– Acting on the CH–NH group of donors 1. 5. 5.– With a quinone or similar compound as acceptor 1. 6. 2.– With a cytochrome as acceptor 1. 6. 5.– With a quinone or similar compound as acceptor 1. 6. 6.– With a nitrogenous group as acceptor 1. 7.–.– Acting on other nitrogenous compounds as donors 1. 7. 2.– With a cytochrome as acceptor 1. 7. 7.– With an iron–sulfur protein as acceptor ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net Table 1 – continued
1. 8.–.– Acting on a sulfur group of donors 1. 8. 2.– With a cytochrome as acceptor 1. 8. 5.– With a quinone or similar compound as acceptor 1. 8. 7.– With an iron–sulfur protein as acceptor 1. 9.–.– Acting on a haem group of donors 1. 9. 6.– With a nitrogenous group as acceptor 1.10.–.– Acting on diphenols and related substances as donors 1.10. 2.– With a cytochrome as acceptor 1.11.–.– Acting on a peroxide as acceptor (peroxidases) 1.11.1.– A single subclass containing the peroxidases 1.12. 2.– With a cytochrome as acceptor 1.13.–.– Acting on single donors with incorporation of molecular oxygen 1.13.11.– With incorporation of two atoms of oxygen 1.13.12.– With incorporation of one atom of oxygen 1.13.99.– Miscellaneous (requires further characterization) 1.14.–.– Acting on paired donors with incorporation of molecular oxygen 1.14.11.– With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors 1.14.12.– With NADH2 or NADPH2 as one donor, and incorporation of two atoms of oxygen into one donor1.14.13.– With NADH2 or NADPH2 as one donor, and incorporation of one atom of oxygen1.14.14.– With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen 1.14.15.– With a reduced iron–sulfur protein as one donor, and incorporation of one atom of oxygen 1.14.16.– With reduced pteridine as one donor, and incorporation of one atom of oxygen 1.14.17.– With ascorbate as one donor, and incorporation of one atom of oxygen 1.14.18.– With another compound as one donor, and incorporation of one atom of oxygen 1.14.99.– Miscellaneous (requires further characterization) 1.15.–.– Acting on superoxide radicals as acceptor 1.18.–.– Acting on reduced ferredoxin as donor ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net Table 1 – continued
1.19.–.– Acting on reduced flavodoxin as donor Note: The Nomenclature Committee has accepted a recommendation that nicotinamide-adenine dinucleotide and nicotinamide-adenine dinucle- otide phosphate should be abbreviated to NAD and NADP, respectively, rather than NAD+ and NADP+, as used previously. In addition toavoiding the erroneous implication that these two compounds will be positively charged at physiological pH values, the reasons for this aregiven in the Newsletter (1996). The reduced forms of these coenzymes are written as NADH and NADPH , rather than NADH and NADPH.
The systematic name is in the form donor:acceptor group- transferase. The recommended names are normally formed Sometimes transferase reactions can be considered in different ways; for example, the general reaction shown Reaction: S-adenosyl-l-methionine 1 3-hexaprenyl- above may be regarded as a transfer of the group Y from X 4,5-dihydroxybenzoate 5 S-adenosyl-l-homocysteine to Z, and would therefore be termed a Y-transferase.
1 3-hexaprenyl-4-hydroxy-5-methoxybenzoate However, it could also be considered as a breaking of the X–Y bond by the introduction of Z. For example, where Z represents phosphate, the process is often referred to as phosphorolysis and the enzyme catalysing the reaction as a Systematic name: S-adenosyl-l-methionine:3-hexapre- phosphorylase. For systematic purposes, these enzymes are nyl-4,5-dihydroxylate O-methyltransferase Comments: Involved in the pathway of ubiquinone The aminotransferase (transaminase) reactions involve synthesis. This enzyme has been listed as EC 2.1.1.64 in some sequence databases; but that enzyme catalyses a containing a carbonyl group, in exchange for the 5 O of R1–CHNH2–R2 1 R3–CO–R4 = R1–CO– These enzymes catalyse the hydrolytic cleavage of bonds such as C–O, C–N, C–C and some other bonds, includingphosphoric anhydride bonds. The overlapping specificitiesof many of these enzymes make it difficult to formulate Thus, the reaction could be regarded as being an oxidative general rules that are applicable to all members of this deamination of the donor (e.g. an amino acid) linked to the class. The systematic name usually takes the form substrate reductive amination of the acceptor (e.g. oxo acid).
X-hydrolase, where X is the group removed by hydrolysis.
Therefore these enzymes might be classified as oxidor- The recommended name is, in many cases, formed by the eductases. However, since the unique distinctive feature of name of the substrate with the suffix -ase. It is understood the reaction is the transfer of the amino group, these that the name of the substrate with this suffix means a enzymes are classified as amino transferases (subclass Hydrolytic enzymes might be classified as transferases, The second figure in the code number of the transferases since hydrolysis itself can be regarded as transfer of a denotes the general nature of the group transferred (a one- specific group to water as the acceptor. Yet, in most cases, carbon group, 2.1; aldehydic or ketonic group, 2.2; acyl the reaction with water as the acceptor was discovered group, 2.3, etc.) and the third number further specifies that earlier and is considered as the main physiological function group (methyltransferase, 2.1.1; formyltransferase, 2.1.2, of the enzyme. This is why such enzymes are classified as etc.). The exception is the case of the enzymes transferring hydrolases rather than as transferases.
phosphorus-containing groups (subclass 2.7), where the The second number indicates the nature of the bond third number specifies the nature of the acceptor group.
hydrolysed, and the third normally specifies the nature of Table 2 summarizes the structure of Class 2.
the substrate, e.g. in the esterases the carboxylic ester ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net hydrolases (3.1.1), thiolester hydrolases (3.1.2), phosphoric (3.4.11–19), with the third figure also depending on the monoester hydrolases (3.1.3); in the glycosidases, the O- catalytic mechanism. A complete list of the peptidases is glycosidases (3.2.1), N-glycosidases (3.2.2), and so on.
now available on-line (see Peptidases, 1998 in Further The peptidases (formerly called peptide hydrolases; Class 3.4.–) cannot be accommodated within this general Subclasses 3.9 - 3.11, which each contain only one or two scheme. It is not even possible to give unambiguous known enzymes, only contain one sub-subclass each, systematic names because of variable specificities and great denoted by the figure 1 (e.g. 3.9.1.1, 3.10.1, 3.10.1.2 etc).
similarities between the actions of different peptidases. The Table 3 summarizes the structure of Class 3.
enzymes are grouped into two sets of sub-subclasses, theendopeptidases (3.4.21–24 and 3.4.99) and exopeptidases Recommended name: 4-hydroxybenzoyl-CoA thioesterase Reaction: 4-hydroxybenzoyl-CoA 1 H2O 5 4-hydro- 2. 1. –.– Transferring one-carbon groups Systematic name: 4-hydroxybenzoyl-CoA hydrolase 2. 1. 2. – Hydroxymethyl-, formyl- and related transferases Comments: This enzyme is part of the bacterial 2,4- 2. 1. 3. – Carboxyl- and carbamoyltransferases 2. 2. –.– Transferring aldehyde or ketone residues 2. 2. 1. – a single subclass containing the transaldolases Reaction: Broad proteolytic activity. With small-mole- cule substrates and inhibitors, the major determinant of specificity is P2, which is preferably Leu, Met 4 Phe, and Other names: cathepsin O and cathepsin X (both misleading, having been used for other enzymes); Cathe- 2. 4.99. – Transferring other glycosyl groups Comments: Prominently expressed in mammalian os- 2. 5. –.– Transferring alkyl or aryl groups, other than methyl teoclasts, and believed to play a role in bone resorption. In 2. 5. 1. – A single subclass that includes a rather mixed NOTE: The specificity of peptidases may be described in terms of a sequence of amino acid residues on either side of 2. 6. –.– Transferring nitrogenous groups the peptide bond that is cleaved (scissile bond), which is 2. 6. 1. – Transaminases (aminotransferases) 2. 6.99. – Transferring other nitrogenous groups 2 2 2 2 P3 2 P2 2 P1P1’ 2 P2’ 2 P3’ 2 C-terminus 2. 7. –.– Transferring phosphorus-containing groups 2. 7. 1. – Phosphotransferases with an alcohol group as 2. 7. 2. – Phosphotransferases with a carboxyl group as These enzymes cleave C–C, C–O, C–N and other bonds by means other than hydrolysis or oxidation. They differ from 2. 7. 3. – Phosphotransferases with a nitrogenous group as other enzymes in that two substrates are involved in one reaction direction but only one in the other. When acting 2. 7. 4. – Phosphotransferases with a phosphate group as on the single substrate, a molecule is eliminated leaving double bonds or rings. The systematic name is formed according to the pattern substrate group-lyase. The hyphen is an important part of the name and, to avoid confusion, 2. 7. 8. – Transferases for other substituted phosphate should not be omitted, e.g. hydro-lyase not ‘hydrolyase’. In the recommended names, expressions like decarboxylase or 2. 7. 9. – Phosphotransferases with paired acceptors aldolase (in case of elimination of CO2 or aldehyde, 2. 8. –.– Transferring sulfur-containing groups respectively) are used. Dehydratase is used for those enzymes catalysing the elimination of water. In cases where the reverse reaction is much more important, or the only one demonstrated, synthase (not synthetase) may be 2. 9. –.– Transferring selenium-containing groups used in the name. Although the term synthetase has ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net Table 3 Class 3.–.–.–. Hydrolases
3.1. 1. – Carboxylic ester hydrolases 3.1. 2. – Thiolester hydrolases 3.1. 3. – Phosphoric monoester hydrolases 3.1. 4. – Phosphoric diester hydrolases 3.1. 5. – Triphosphoric monoester hydrolases 3.1. 6. – Sulfuric ester hydrolases 3.1. 7. – Diphosphoric monoester hydrolases 3.1. 8. – Phosphoric triester hydrolases 3.1.11. – Exodeoxyribonucleases producing 5′-phosphomonoesters 3.1.13. – Exoribonucleases producing 5′-phosphomonoesters 3.1.14. – Exoribonucleases producing other than 5′-phosphomonoesters 3.1.15. – Exonucleases active with either ribo- or deoxyribonucleic acids and producing 5′-phosphomonoesters 3.1.16. – Exonucleases active with either ribo- or deoxyribonucleic acids and producing other than 5′-phosphomonoesters 3.1.21. – Endodeoxyribonucleases producing 5′-phosphomonoesters 3.1.22. – Endodeoxyribonucleases producing other than 5′-phosphomonoesters 3.1.25. – Site-specific endodeoxyribonucleases specific for altered bases 3.1.26. – Endoribonucleases producing 5′-phosphomonoesters 3.1.27. – Endoribonucleases producing other than 5′-phosphomonoesters 3.1.30. – Endonucleases active with either ribo- or deoxyribonucleic acid and producing 5′-phosphomonoesters 3.1.31. – Endonucleases active with either ribo- or deoxyribonucleic acid and producing other than 5′-phosphomonoesters 3.2. 1. – Hydrolysing O-glycosyl compounds 3.2. 2. – Hydrolysing N-glycosyl compounds 3.2. 3. – Hydrolysing S-glycosyl compounds 3.3. 1. – Thioether hydrolases 3.3. 2. – Ether hydrolases 3. 4. –.– Acting on peptide bonds (peptidase) 3.4.11. – Aminopeptidases 3.4.13. – Dipeptidases 3.4.14. – Dipeptidyl-peptidases and tripeptidyl-peptidases 3.4.15. – Peptidyl-dipeptidases 3.4.16. – Serine-type carboxypeptidases 3.4.17. – Metallocarboxypeptidases 3.4.18. – Cysteine-type carboxypeptidases 3.4.19. – Omega peptidases 3.4.21. – Serine endopeptidases 3.4.22. – Cysteine endopeptidases 3.4.23. – Aspartic endopeptidases 3.4.24. – Metalloendopeptidases 3.4.99. – Endopeptidases of unknown catalytic mechanism 3. 5. –.– Acting on carbon–nitrogen bonds, other than peptide bonds 3.5. 1. – In linear amides 3.5. 2. – In cyclic amides 3.5. 3. – In linear amidines 3.5. 4. – In cyclic amidines 3.5. 5. – In nitriles 3.5.99. – In other compounds ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net Table 3 – continued
3.6. 1. – In phosphorus-containing anhydrides 3.6. 2. – In sulfonyl-containing anhydrides 3. 7. –.– Acting on carbon–carbon bonds 3. 9. –.– Acting on phosphorus–nitrogen bonds3.10. –.– Acting on sulfur–nitrogen bonds3.11. –.– Acting on carbon–phosphorus bonds3.12. –.– Acting on sulfur–sulfur bonds sometimes been used in the names of enzymes from this indicates the bond broken: 4.1 are carbon–carbon lyases, class, that use is discouraged in order to prevent confusion 4.2 are carbon–oxygen lyases, and so on. The third figure with enzymes from Class 6 (see below).
gives further information on the group eliminated (e.g.
Various subclasses of the lyases include pyridoxal- phosphate enzymes that catalyse the elimination of a b- Table 4 summarizes the structure of Class 4.
or g-substituent from an a-amino acid, followed by a replacement of this substituent by some other group. In the overall replacement reaction, no unsaturated end productis formed; therefore, these enzymes might formally be classified as alkyltransferases (EC 2.5.1.-). However, there Reaction: 2-hydroxyisobutyronitrile 5 cyanide 1 is ample evidence that the replacement is a two-step reaction involving the transient formation of enzyme- Other name(s): hydroxynitrile lyase; oxynitrilase bound a,b- (or b,g-)unsaturated amino acids. According to Systematic name: 2-hydroxyisobutyronitrile acetone- the rule that the first reaction is indicative for classification, these enzymes are correctly classified as lyases. Examples Comments: The enzyme from Hevea (rubber tree) and are tryptophan synthase (EC 4.2.1.20) and cystathionine b- Manihot spp. (cassava) accepts aliphatic and aromatic lyase (EC 4.2.1.22). The second figure in the code number hydroxynitriles, unlike EC 4.1.2.11, which does not act onaliphatic Table 4 Class 4. –.–.– Lyases
(acetone cyanohydrin) is liberated by glycosidase actionon linamarin These enzymes catalyse geometric or structural changes within one molecule. According to the type of isomerism involved they may be called racemases, epimerases, cis– trans-isomerases, isomerases, tautomerases, mutases or cycloisomerases. The second number denotes the type of isomerism involved, and the third number the type ofsubstrate. In some cases, the reaction involves an intermolecular oxidoreduction, but since the donor and acceptor groups are in the same molecule they are classified as isomerases rather than oxidoreductases, even though they may contain firmly bound NAD or NADP.
4. 3.99 – Other carbon–nitrogen-lyases Table 5 summarizes the structure of Class 5.
Recommended name: a-methylacyl-CoA racemase ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net Table 5 Class 5. –.–.– Isomerases
5. 1. 1. – Acting on amino acids and derivatives Recommended name: 4-chlorobenzoate-CoA ligase Reaction: 4-chlorobenzoate 1 CoA 1 ATP 5 4- 5. 1. 2. – Acting on hydroxy acids and derivatives 5. 1. 3. – Acting on carbohydrates and derivatives Systematic name: 4-chlorobenzoate : CoA ligase Comments: Requires Mg2 1 . This enzyme is part of the 5. 2. –.– cis–trans-Isomerases bacterial 2,4-dichlorobenzoate degradation pathway.
5. 3. –.– Intramolecular oxidoreductases 5. 3. 1. – Interconverting aldoses and ketoses 5. 3. 2. – Interconverting keto- and enol-groups 5. 3. 3. – Transposing C=C bonds5. 3. 4. – Transposing S–S bonds Isoenzymes may not be easily accommodated in any 5. 3.99. – Other intramolecular oxidoreductases system of classification simply in terms of reaction 5. 4. –.– Intramolecular transferases (mutases) catalysed. For example, there are about 20 differentisoenzymes of alcohol dehydrogenase in human liver.
These have been organized into broad classes in terms of 5. 4. 2. – Phosphotransferases (phosphomutases) their electrophoretic mobilities and, more precisely, in terms of their sequences and genetic origin. These classes show very different chain-length specificities for primary aliphatic alcohols and also different inhibitor specificities.
However, since they all oxidize primary alcohols and havea strong preference towards NAD as the coenzyme, theyare all grouped together under the general heading of EC1.1.1.1. Furthermore, problems also arise from species Reaction: (2S)-2-methylacyl-CoA 5 (2R)-2-methyla- differences; for example, class EC 1.1.1.1 includes NAD- dependent alcohol dehydrogenases from all species, Systematic name: 2-methylacyl-CoA 2-epimerase although the mammalian liver and yeast enzymes, for Comments: a-methyl-branched acyl-CoA derivatives example, are profoundly different in structure and with chain lengths of more than C10 are substrates. Also behaviour. Only when isoenzymes have very different active towards some aromatic compounds (e.g. ibuprofen) substrate specificities might classification by function and bile acid intermediates, such as trihydroxycoprosta- provide the whole solution. For example, liver glucokinase is now recognized to be a member of the hexokinase familyof isoenzymes (hexokinase type IV) and is classified as ahexokinase (EC 2.7.1.1), whereas the name glucokinase These enzymes catalyse the joining together (ligating) of two molecules with the concomitant hydrolysis of a 6. 1. –.– Forming carbon–oxygen bonds diphosphate bond in ATP or a similar triphosphate. The 6. 1. 1. – Ligases forming aminoacyl-tRNA and related systematic enzyme name takes the form A:B ligase (XDP- or XMP-forming). The recommended name often takes the 6. 2. –.– Forming carbon–sulfur bonds form A–B ligase. Sometimes the name synthase is used for the recommended name to emphasize the synthetic nature 6. 3. –.– Forming carbon–nitrogen bonds of the reaction, which can also be helpful if the reaction is 6. 3. 1. – Acid–ammonia (or amine) ligases (amide complex. The name synthetase is also sometimes used instead of synthase in the names of enzymes in this class.
6. 3. 2. – Acid–amino-acid ligases (peptide synthases) The second figure in the code number indicates the bond formed: 6.1 for C–O bonds (enzymes acylating tRNA), 6.2 6. 3. 4. – Other carbon–nitrogen ligases for C–S bonds (acyl-CoA derivatives), etc. Sub-subclasses 6. 3. 5. – Carbon–nitrogen ligases with glutamine as are only in use in the C–N ligases (6.3), which include the amide synthases (6.3.1), the peptide synthases (6.3.2), 6. 4. –.– Forming carbon–carbon bonds enzymes forming heterocyclic rings (6.3.3), etc.
6. 5. –.– Forming phosphoric ester bonds Table 6 summarizes the structure of Class 6.
ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net (EC 2.7.1.2) is specifically recommended for the enzyme from invertebrates and microorganisms that has a highspecificity for glucose. In other cases, this problem is being Alberty RA, Cornish-Bowden A, Gibson QH et al. (1996) Recommen- dations for nomenclature and tables in biochemical thermodynamics.
addressed by linking the electronic form of the enzyme list European Journal of Biochemistry 240: 1–14.
to other appropriate databases, based on structural Dixon M and Webb EC (1958) Enzymes, pp. 183–227. London: Enzyme Nomenclature (1992) Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. NewYork: Academic Press.
Enzyme Supplements (1999) Prepared for the NC-IUBMB by Tipton New enzymes and new functions of existing enzymes are KF and Boyce S. [http://www.chem.qmw.ac.uk/iubmb/enzyme/] being discovered at a rapid pace and work on revising and IUBMB Nomenclature Committee Enzyme Nomenclature. Recom- expanding the list of enzymes is a continuing operation.
mendations of the Nomenclature Committee of the International Suggestions for enzymes that should be included, or for revisions and corrections to existing entries can be Newsletter (1996) of the IUPAC-IUBMB Joint Commission on submitted electronically using forms available through Biochemical Nomenclature (JCBN) and Nomenclature Committee the IUBMB Nomenclature Committee Enzyme Nomen- of IUBMB (NC-IUBMB). Archives of Biochemistry and Biophysics clature or SWISSPROT ENZYME home pages. Alter- (1997) 344: 242–252; Biochemical Journal (1997) 327: 311–319; natively, material for all enzyme classes except the Chemistry International (1997) 19: 116–119; European Journal of peptidases (Class 3.4. –.–) can be sent by e-mail or regular Biochemistry (1997) 247: 733–739; Glycoconjugate Journal (1998) 15: mail to Dr Sinead Boyce (Department of Biochemistry, 637–647. Also available on-line at [http://www.chem.qmw.ac.uk/iubmb/newsletter/] Trinity College, Dublin 2, Ireland; E-mail: sboyce@tcd.ie).
Panico R, Richer J-C Powell WH (1994) A Guide to IUPAC Material relating to the peptidases should be sent to Dr Nomenclature of Organic Compounds. Oxford: Blackwell Science.
Alan J. Barrett (Peptidase Laboratory, Department of Peptidases (1998) Prepared for the NC-IUBMB by Barrett AJ, Bond JS, Immunulogy, Babraham Institute, Babraham CB2 4AT, Fiedler F et al. [http://www.chem.qmw.ac.uk/iubmb/enzyme/EC34/] UK; E-mail; alan.barrett@bbsrc.ac.uk). After these have SWISSPROT ENZYME. Swiss Institute of Bioinformatics (SIB) been checked and considered by the Nomenclature Enzyme nomenclature database primarily based on the recommenda- Committee as a whole, they are incorporated into the tions of the Nomenclature Committee of the International Union ofBiochemistry and Molecular Biology (IUBMB) [http://www.expa- Enzyme Nomenclature database, which is being prepared ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

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