Active site

In molecular biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues (or nucleotides in ribozymes) that participate in recognition of the substrate. Residues that directly participate in the catalytic reaction mechanism are called active site residues.



Binding mechanism
There are two proposed models of how enzymes work: the lock and key model and the induced fit model. The lock and key model assumes that the active site is a perfect fit for a specific substrate and that once the substrate binds to the enzyme no further modification is necessary; this is simplistic. The induced fit model is a development of the lock-and-key model and instead assumes that an active site is more flexible and that the presence of certain residues (amino acids) in the active site will encourage the enzyme to locate the correct substrate, after which conformational changes may occur as the substrate is bound.

Chemistry
Substrates bind to the active site of the enzyme or a specificity pocket through hydrogen bonds, hydrophobic interactions, temporary covalent interactions (van der Waals) or a combination of all of these to form the enzyme-substrate complex. Residues of the active site will act as donors or acceptors of protons or other groups on the substrate to facilitate the reaction. In other words, the active site modifies the reaction mechanism in order to change the activation energy of the reaction. The product is usually unstable in the active site due to steric hindrances that force it to be released and return the enzyme to its initial unbound state.