Substrate specificity

The properties  and spatial arrangement  of the amino acid residues forming the active  site  of  an  enzyme  will  determine  which  molecules  can  bind  and  be substrates for which enzyme. The Substrate specificity is frequently determined through changes in associatively few amino acids in the active site. This is obviously seen in the three digestive enzymes chymotrypsin, trypsin and elastase.  These three  enzymes  belong  to  a  family  of  enzymes  called  the  serine  proteases  –‘serine’  because  they  have  a serine  residue  in  the  active  site  that  is critically involved  in  catalysis  and  ‘proteases’  because  they  catalyze  the  hydrolysis  of peptide  bonds in proteins.  All of three enzymes cleave peptide bonds in protein substrates on the carboxyl side of certain amino acid residues.

Trypsin   cleaves   on  the  carboxyl   side  of  positively   charged   Arg or Lys residues, chymotrypsin cleaves on the carboxyl side of bulky hydrophobic  and aromatic amino acid residues  and elastase  cleaves  on the carboxyl  side of residues with small uncharged side-chains. Their conflicting specificities are determined through the nature of the amino acid groups in their substrate binding sites that are complementary to the substrates upon that they act. Therefore trypsin has a negatively  charged  Asp residue  in its substrate  binding  site that interacts with  the positive  charge  on the Arg and Lys side-chains  of the substrate. Chymotrypsin has amino acid residues with small side-chains, like as Gly and Ser, in its substrate binding site which allows access of the bulky side-chain of the substrate. In contrast, elastase has the relatively large uncharged amino acid side-chains of Val and Thr protruding into its substrate binding site avoiding access of all but the small side-chains on Gly and Ala.