How Enzymes Work? – PDB/RCSB

Enzymes are a catalytic subgroup of proteins formed as end products of the Central Dogma of biology. They are essential for cellular functioning.

Here in this Protein Data Bank (PDB) video the enzymes constituting the hugely important metabolic pathway –the citric acid cycle– that connects carbohydrate, fat and protein metabolism are briefly visualized. Subsequently, the enzyme aconitase (aconitate hydratase; EC 4.2.1.3) in this hugely important metabolic pathway is highlighted as an example. The steps taking place in the active site of this enzyme is shown in great detail while catalyzing the reaction.

Enzymes are key players of metabolic pathways. Together with proteins they form a very large fraction of molecular processes. There are 6 major reaction types designated by the Enzyme Commission (EC):

EC 1 Oxidoreductases: catalyze oxidation/reduction reactions

EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate group)

EC 3 Hydrolases: catalyze the hydrolysis of various bonds

EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation

EC 5 Isomerases: catalyze isomerization changes within a single molecule

EC 6 Ligases: join two molecules with covalent bonds.

Perhaps one of the most intensively studied enzyme is the 12 subunit eukaryotic RNA Polymerase II responsible from reading the genetic code on DNA and synthesize mRNA. Some enzymes can have quite impressive physical properties such as the cargo carrying motor proteins featured prominently in the 3-D virtual reality animation a virtual tour of the cell.

You can learn more about chemistry of biological molecules in the Molecular Nature category.