What’s in a name?

What’s in a name? That which we call lactate dehydrogenase by any other name would still convert lactate to pyruvate; so would EC 2.4.1.11 (glycogen synthase) were it not EC 2.4.1.11 call’d…..

I think many people share these sentiments when it comes to the naming of enzymes. I really don’t think that it matters whether the enzyme is coded and classified or just named for its function. For all that matters I have no problem calling the enzyme in each reaction as enzyme 1 or glucose breaker.

But alas, if life were so easy then there would be a lot of chaos in the scientific world since what I will be calling hexokinase in glycolysis, some person in Australia might be calling it Bob’s enzyme. Therefore for sake of convenience and standardization, there has been a system created to assign names to all the known enzymes.

Now, pay close attention cause I will attempt to breakdown this whole nomenclature business with enzymes. Enzyme nomenclature is assigned by two names: recommended name and systematic name.

Recommended name is the commonly referred to names or most recognized names based on their function, their substrate or just by who discovered them/random naming. You might see the problems here with lack of uniformity and a bit of confusion in the naming. Examples of this type of naming may include lipases (enzymes involved in the metabolism of lipids), pyruvate decarboxylase (removes the carboxylic acid group to form carbon dioxide) or even trypsin (hydrolysis of peptide bonds).

Systematic name was developed by the International Union of Biochemistry and Molecular Biology (IUBMB). This group of biochemists came together in a joint committee and decided that it was time to standardize and codify enzymes. The main purpose was to facilitate better communication of all biochemical information and research by having a standard generally understood nomenclature and description of enzymes. In 1955, they devised a system of nomenclature that divided all enzymes into 6 major classes and then subdivisions within each class. These names were based completely on the reaction to which the enzyme catalyses and includes all the substrates involved as well. This provided a comprehensive and informative method to which enzymes may be named. This name was also codified for specificity and reference. However, this is quite a mouthful to use and still enzymes are usually referred to by their recommended names.

Below is an illustration of the 6 major classes of the systematic nomenclature.

Before I begin, you might be wondering well, how am I going to remember these 6 classes? Well, I have devised a mnemonic, which is slightly rude, but don’t judge me, because I think that the ruder mnemonics are, the more they are remembered.

Okay, so there are 6 major classes:

  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases

So, taking the first letter from each class we have:

Only

Two

Happy

Lovers

Indulge in

Lovemaking

All right, so that may aid in remembering the order of the classes, but unfortunately, we still have to learn the details of each class. Also knowing the class, will aid in understanding the coded name for the enzyme. This coded name is known as the ENZYME COMMISSION NUMBER (EC number). The EC number can be broken-down as follows:

Using the example of glycogen synthase

EC 2.4.1.11

2: represents the class to which it belongs; transferases

4: represents the subclass that transfers carbon-groups to the glycogen

1: sub-subclass

11: serial number

This gives insight into the specific action of the enzyme.

Right, now that all that is out of the way, let us now focus on each class, where I will give a brief description of each and follow with an example.

  1. Oxidoreductases: as the name implies these enzymes catalyse oxidation- reduction reactions (redox reactions). Example: alcohol dehydrogenase. This enzyme facilitates the conversion of alcohols to aldehydes by reduction of NAD  to NADH. Its systematic name is alcohol: NAD+ oxidoreductase. Its EC number is EC 1.1.1.1
  2. Transferases: these enzymes catalyse the transfer of carbon, nitrogen or phosphate groups in a reaction. Example: tRNA (cytosine-5-)-methyltransferase. This enzyme facilitates the conversion of S-adenosyl-L-methionine to S-adenosyl-L-homocysteine by transferring a methyl group from methionine. Its systematic name is S-adenosyl-L-methionine: tRNA (cytosine-5-)-methyltransferase. Its EC number is EC 2.1.1.29
  3. Hydrolases: these catalyse the cleavage of bonds by the addition of water molecules. Example: acetylcholinesterase. This enzyme facilitates the degradation of the neurotransmitter acetylcholine to acetate, choline and hydrogen ions by addition of water molecule. Its systematic name is acetylcholine acetylhydrolase. Its EC number is EC 3.1.1.7
  4. Lyases: these catalyse the cleavage of C-C, C-S and certain C-N bonds by other means than hydrolysis and oxidation. Example: carnitine decarboxylase. This enzyme facilitates the degradation of carnitine to 2-metylcholine by the cleavage of the C-C bonds to form carbon dioxide. Its systematic name is carnitine carboxy-lyase (2-methylcholine forming). Its EC number is EC 4.1.1.42
  5. Isomerases: these catalyse the racemization (conversion of an enantiomer to another enantiomer) of optical or geometric isomers. Example: ribose-5-phosphate isomerase. This facilitates the conversion of D-ribose 5-phosphate to D-ribulose 5 phosphate. This involves the conversion of the pentose sugar from the aldose form to the ketose form. Its systematic name is D-ribose-5-phosphate aldose-ketose-isomerase. The EC number is EC 5.3.1.6
  6. Ligases: these catalyse the formation of bonds between carbon atoms and O, S, N atoms that are coupled with the hydrolysis of high-energy phosphate groups. Example: succinyl-CoA synthetase (ADP forming). This enzyme facilitates the conversion of succinate to succinyl-CoA and driving the formation of ADP by the cleavage of the phosphate group from ATP. The systematic name is succinate-CoA ligase (ADP-forming). The EC number is EC 6.2.1.5

Well, well, well. That was a lot to take in but read it through and understand that basics of the classes and the EC classification. I really hope that this review helps and did not confuse you at all.

I believe that you can now realize the importance of the nomenclature of enzymes. Peace out for now people and enjoy the biochem.

 

References

 

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One thought on “What’s in a name?

  1. theladyhum says:

    Hey, this is really cool and informative =)

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