EC numbers and enzyme colors

How enzymes are named by what they do, and what the color of an enzyme model tells you

What an EC number is

The Enzyme Commission (EC) gives every enzyme-catalyzed reaction a number of four parts, such as EC 2.6.1.52. The number describes the reaction, so two proteins from different species that catalyze the same reaction share one number. A protein that catalyzes two reactions has two numbers.

2.6.1.52

First number: the type of reaction. There are six types, listed below. This is the number the colors follow.
Second number: the subclass. It names the kind of group or bond involved. For type 2 (transferases), 2.6 moves nitrogen groups, and 2.7 moves phosphate groups.
Third number: the sub-subclass. It narrows the group, the acceptor or the cofactor. In 2.6.1 the group is an amino group moved between two compounds.
Fourth number: the serial number of the enzyme within its sub-subclass, handed out in the order of registration. It carries no chemical meaning.

Phosphoserine aminotransferase (EC 2.6.1.52), which makes a step of serine synthesis, moves an amino group from glutamate to 3-phosphohydroxypyruvate. The numbers say this: type 2 transfer, of nitrogen groups, as an amino group, entry 52.

The EC list covers reactions, so a number does not identify one protein, one gene or one species. Databases sometimes still list an older number for a structure. Where a card here differs from the number in the PDB entry, the card uses the current number.

The six colors

Every enzyme model in the pathways is colored by the first EC number. The same six colors mark the enzyme tiles in the soup and the enzyme models in the 3D card.

Oxidoreductases

Move electrons, often as hydrogen, between molecules. They use cofactors such as NAD⁺, NADP⁺ and FAD, which is why these cofactors turn up beside an arrow.

Example: phosphoglycerate dehydrogenase, EC 1.1.1.95 (first step of serine synthesis).

Transferases

Move a chemical group from one molecule to another: an amino group, a phosphate group, a one-carbon unit. Kinases and aminotransferases belong here.

Example: phosphoserine aminotransferase, EC 2.6.1.52.

Hydrolases

Break a bond by adding water. Phosphatases, proteases and nucleases are hydrolases.

Example: phosphoserine phosphatase, EC 3.1.3.3.

Lyases

Split or form a bond without water and without an oxidation, often leaving a double bond or closing a ring. Dehydratases and decarboxylases belong here.

Example: enolase, EC 4.2.1.11 (removes water from 2-phosphoglycerate).

Isomerases

Rearrange one molecule into an isomer with the same atoms in a different arrangement. Mutases, epimerases and racemases belong here.

Example: triose phosphate isomerase, EC 5.3.1.1.

Ligases

Join two molecules and pay for it with the energy of ATP or a similar compound. Many biosynthetic steps end with a ligase.

Example: glutamine synthetase, EC 6.3.1.2.

A seventh type, translocases (EC 7), moves ions or molecules across a membrane. No enzyme in the pathways here belongs to it.