Benzoyl-L-arginine amide

PAD4 is a Ca -dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. (a) Ribbon representation of the PAD4/benzoyl-L-arginine amide complex (PDB code Iwda) in the presence of the ions (green spheres). 

The structural basis for recognition of protein substrates is not yet clear. However, structures of PAD4 in complex with A -benzoyl-L-arginine amide and peptides from histones H3 and H4 that are known to he citrullinated have provided clues as to how PAD4 hinds and recognizes small molecule substrates. As with ADI and DDAH, the arginine residue of the substrate binds at the center of the propeller of the catalytic domain, and the conserved core residues interact with the guanidine side chain. ... 

We have shown by a comparison of the pH dependence of the step characterized by ki that the hydrolysis of the enzyme-acyl compound is the rate-determining step for the enzymatic hydrolysis of the usual amino acid amide substrates. In the case of chymotrypsin, acetyl-L-phenylalanine ethyl ester is hydrolyzed 1,000 times faster than the corresponding amide and in the case of trypsin, benzoyl-L-arginine ethyl ester is hydrolyzed 300 times faster than the corresponding amide. This suggests that for the amide hydrolysis too the second step, the acylation of the enzyme, must be the rate-determining step, since the third step is obviously identical for esters and amides of the same amino acid derivatives. The pH dependence of the chymotrypsin-catalyzed hydrolysis of acetyl-L-tyrosine ethyl ester and acetyl-L-phenylalanine ethyl ester indicates that for these reactions ki and kz are of the same order of magnitude and both contribute to the over-all rate, as shown by Equation (4). 

---