Crystal structure of a subtilisin BPN′ complex with N-benzoyl- l-arginine

Abstract

The structure of a complex between subtilisin BPN′ and the product-inhibitor N-benzoyl- l-arginine has been determined from a 2.5-Å electron-density difference map. The inhibitor is bound adjacent to the catalytic site of the enzyme with its carboxylate group 3 Å from the reactive Ser 221 side chain, and its amido NH forming a hydrogen bond with the backbone CO of Asn 218. The guanidinium group of the inhibitor lies parallel to and in van der Waals contact with the exposed side chain of Tyr 217. This binding geometry is different from that observed in peptide chloromethyl ketone derivatives of subtilisin. Possible interpretations are, either that the new geometry represents an alternative productive binding mode, or that it represents an important non-productive binding mode for N-benzoyl- l-arginine esters and amides.