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Enzyme Nomenclature

Traditionally, enzymes often were named by adding the suffix-ase to the name of the substrate upon which they acted, as in urease for the urea-hydrolyzing enzyme or phosphatase for enzymes hydrolyzing phosphoryl groups from organic phosphate compounds. Other enzymes acquired names bearing little resemblance to their activity, such as the peroxide-decomposing enzyme catalase or the proteolytic enzymes (proteases) of the digestive tract, trypsin and pepsin. Because of the confusion that arose from these trivial designations, an International Commission on Enzymes was established in 1956 to create a systematic basis for enzyme nomenclature. Although common names for many enzymes remain in use, all enzymes now are classified and formally named according to the reaction they catalyze. Six classes of reactions are recognized (Table 14.1).

Table 14.1
Systematic Classification of Enzymes According to the Enzyme Commission
E.C. Number Systematic Name and Subclasses
Oxidoreductases (oxidation–reduction reactions)
1.1 Acting on CH—OH group of donors
1.1.1 With NAD or NADP as acceptor
1.1.3 With O2 as acceptor
1.2 Acting on the group of donors
1.2.3 With O2 as acceptor
1.3 Acting on the CH—CH group of donors
1.3.1 With NAD or NADP as acceptor
Transferases (transfer of functional groups)
2.1 Transferring C-1 groups
2.1.1 Methyltransferases
2.1.2 Hydroxymethyltransferases and formyltransferases
2.1.3 Carboxyltransferases and carbamoyltransferases
2.2 Transferring aldehydic or ketonic residues
2.3 Acyltransferases
2.4 Glycosyltransferases
2.6 Transferring N-containing groups
2.6.1 Aminotransferases
2.7 Transferring P-containing groups
2.7.1 With an alcohol group as acceptor
Hydrolases (hydrolysis reactions)
3.1 Cleaving ester linkage
3.1.1 Carboxylic ester hydrolases
3.1.3 Phosphoric monoester hydrolases
3.1.4 Phosphoric diester hydrolases
Lyases (addition to double bonds)
4.1 C=C lyases
4.1.1 Carboxy lyases
4.1.2 Aldehyde lyases
4.2 C=O lyases
4.2.1 Hydrolases
4.3 C=N lyases
4.3.1 Ammonia-lyases
Isomerases (isomerization reactions)
5.1 Racemases and epimerases
5.1.3 Acting on carbohydrates
5.2 Cis-trans isomerases
Ligases (formation of bonds with ATP cleavage)
6.1 Forming C—O bonds
6.1.1 Amino acid–RNA ligases
6.2 Forming C—S bonds
6.3 Forming C—N bonds
6.4 Forming C—C bonds
6.4.1 Carboxylases

Within each class are subclasses, and under each subclass are sub-subclasses within which individual enzymes are listed. Classes, subclasses, sub-subclasses, and individual entries are each numbered, so that a series of four numbers serves to specify a particular enzyme. A systematic name, descriptive of the reaction, is also assigned to each entry. To illustrate, consider the enzyme that catalyzes this reaction:



ATP + d-glucose ® ADP + d-glucose-6-phosphate

A phosphate group is transferred from ATP to the C-6-OH group of glucose, so the enzyme is a transferase (Class 2, Table 14.1). Subclass 7 of transferases is enzymes transferring phosphorus-containing groups, and sub-subclass 1 covers those phosphotransferases with an alcohol group as an acceptor. Entry 2 in this sub-subclass is ATP: d-glucose-6-phosphotransferase, and its classification number is 2.7.1.2. In use, this number is written preceded by the letters E.C., denoting the Enzyme Commission. For example, entry 1 in the same sub-subclass is E.C.2.7.1.1, ATP: d-hexose-6-phosphotransferase, an ATP-dependent enzyme that transfers a phosphate to the 6-OH of hexoses (that is, it is nonspecific regarding its hexose acceptor). These designations can be cumbersome, so in everyday usage, trivial names are employed frequently. The glucose-specific enzyme, E.C.2.7.1.2, is called glucokinase and the nonspecific E.C.2.7.1.1 is known as hexokinase. Kinase is a trivial term for enzymes that are ATP-dependent phosphotransferases.

Coenzymes

Many enzymes carry out their catalytic function relying solely on their protein structure. Many others require nonprotein components, called cofactors (Table 14.2). Cofactors may be metal ions or organic molecules referred to as coenzymes. Cofactors, because they are structurally less complex than proteins, tend to be stable to heat (incubation in a boiling water bath). Typically, proteins are denatured under such conditions. Many coenzymes are vitamins or contain vitamins as part of their structure. Usually coenzymes are actively involved in the catalytic reaction of the enzyme, often serving as intermediate carriers of functional groups in the conversion of substrates to products. In most cases, a coenzyme is firmly associated with its enzyme, perhaps even by covalent bonds, and it is difficult to separate the two. Such tightly bound coenzymes are referred to as prosthetic groups of the enzyme. The catalytically active complex of protein and prosthetic group is called the holoenzyme. The protein without the prosthetic group is called the apoenzyme; it is catalytically inactive.

Table 14.2
Enzyme Cofactors: Some Metal Ions and Coenzymes and the Enzymes with Which They Are Associated
Metal Ions and Some Enzymes That Require Them Coenzymes Serving as Transient Carriers of Specific Atoms or Functional Groups Representative Enzymes Using Coenzymes
Metal Ion Enzyme Coenzyme Entity Transferred  
Fe2+ or Fe3+ Cytochrome oxidase Catalase Peroxidase Thiamine pyrophosphate (TPP) Flavin adenine dinucleotide (FAD) Nicotinamide adenine dinucleotide (NAD) Aldehydes Hydrogen atoms Hydride ion (H-) Pyruvate dehydrogenase Succinate dehydrogenase Alcohol dehydrogenase
Cu2+ Cytochrome oxidase      
Zn2+ DNA polymerase Carbonic anhydrase Coenzyme A (CoA) Pyridoxal phosphate (PLP) Acyl groups Amino groups Acetyl-CoA carboxylase Aspartate aminotransferase
  Alcohol dehydrogenase 5'-Deoxyadenosylcobalamin (vitamin B12) H atoms and alkyl groups Methylmalonyl-CoA mutase
Mg2+ Hexokinase Glucose-6-phosphatase Biotin (biocytin) CO2 Propionyl-CoA carboxylase
Mn2+ Arginase Tetrahydrofolate (THF) Other one-carbon groups Thymidylate synthase
K+ Pyruvate kinase (also requires Mg2+)      
Ni2+ Urease      
Mo Nitrate reductase      
Se Glutathione peroxidase      

Date: 2016-01-03; view: 598


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