<P> Catalytic triads perform covalent catalysis using a residue as a nucleophile . The reactivity of the nucleophilic residue is increased by the functional groups of the other triad members . The nucleophile is polarised and oriented by the base, which is itself bound and stabilised by the acid . </P> <P> Catalysis is performed in two stages . First, the activated nucleophile attacks the carbonyl carbon and forces the carbonyl oxygen to accept an electron, leading to a tetrahedral intermediate . The build - up of negative charge on this intermediate is typically stabilized by an oxanion hole within the active site . The intermediate then collapses back to a carbonyl, ejecting the first half of the substrate, but leaving the second half still covalently bound to the enzyme as an acyl - enzyme intermediate . The ejection of this first leaving group is often aided by donation of a proton by the base . </P> <P> The second stage of catalysis is the resolution of the acyl - enzyme intermediate by the attack of a second substrate . If this substrate is water then the result is hydrolysis; if it is an organic molecule then the result is transfer of that molecule onto the first substrate . Attack by this second substrate forms a new tetrahedral intermediate, which resolves by ejecting the enzyme's nucleophile, releasing the second product and regenerating free enzyme . </P> <P> The side - chain of the nucleophilic residue performs covalent catalysis on the substrate . The lone pair of electrons present on the oxygen or sulphur attacks the electropositive carbonyl carbon . The 20 naturally occurring biological amino acids do not contain any sufficiently nucleophilic functional groups for many difficult catalytic reactions . Embedding the nucleophile in a triad increases its reactivity for efficient catalysis . The most commonly used nucleophiles are the hydroxyl (OH) of serine and the thiol / thiolate ion (SH / S) of cysteine . Alternatively, threonine proteases use the secondary hydroxyl of threonine, however due to steric hindrance of the side chain's extra methyl group such proteases use their N - terminal amide as the base, rather than a separate amino acid . </P>

In the serine protease active site which amino acids form the catalytic triad