Specificity and Promiscuity in Enzyme Superfamilies

Abstract

In order to identify and assess sequence markers that support enzyme structure and specificity, we have undertaken the study of enzyme superfamilies, namely the enzymes from the Haloalkanoate Dehalogenase (HAD) superfamily and the thioesterases of the hotdog‐fold superfamily. Because of the number of homologues within each organism in these families the members provide numerous examples of iso‐functional orthologues to study determinants of specificity and paralogues to study function diversification. Although specificity is often considered the hallmark of enzymes, the occurrence of enzymes displaying substrates promiscuity or substrate ambiguity can offer advantages to the cell. Indeed there may be selective pressures that favor the occurrence of promiscuous enzymes. Examples from the HADSF and thioesterases show that promiscuity can provide the cell ways to perform housekeeping functions and a means of bypassing blocked steps in metabolic pathways. In order to obtain a “panoramic view of promiscuity”, we have employed large‐scale substrate screening on a diverse set of HADSF enzymes and hotdog‐fold thioesterases from a sampling of bacteria across phyla. The screens have uncovered orthologs of known enzymes and revealed some new pathways and activities. The results highlight that promiscuity is much more prevalent than one might imagine. The HADSF and thioesterases exemplify two different ways that enzyme structure can act to promote substrate promiscuity.