The E. coli NudL enzyme is a Nudix hydrolase that cleaves CoA and its derivatives

Abstract

The process of bacterial coenzyme A (CoA) degradation has remained unknown despite the otherwise detailed characterization of the CoA synthesis pathway over 30 years ago. Numerous enzymes capable of CoA degradation have been identified in other domains of life that belong to the Nudix superfamily of hydrolases, but the molecule responsible for this process in the model bacterial system of E. coli remains a mystery. We report here that E. coli contains two such Nudix enzymes capable of CoA degradation into 4-phosphopantetheine and 3,5-adenosine monophosphate. The E. coli enzymes NudC and NudL were cloned in various promoter-fusion constructs in order to purify them as soluble active enzymes and characterize their ability to catalyze the phosphohydrolysis of CoA. NudC, an enzyme known to hydrolyze NADH as its principal substrate, demonstrated the ability to hydrolyze CoA, among other coenzymes, at comparable rates to eukaryotic Nudix hydrolases. NudL, a previously uncharacterized enzyme, demonstrated the ability to cleave only CoA and CoA-related molecules at a rate orders of magnitude slower than its eukaryotic orthologs. NudC and NudL therefore represent a previously uncharacterized pathway of CoA degradation in the highly studied E. coli system. While the two enzymes display some substrate overlap, their respective activities imply that NudC may play a role as a general coenzyme hydrolase, while NudL specifically targets CoA. These data further suggest a role for these enzymes in the regulation of bacterial CoA-RNA.