Abstract
Glycyl radical enzymes (GREs) represent a diverse superfamily of enzymes that utilize a radical mechanism to catalyze difficult, but often essential, chemical reactions. In this work we present the first biochemical and structural data for a GRE-type diol dehydratase from the organism Roseburia inulinivorans (RiDD). Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is in fact a diol dehydratase. In addition, the RiDD will utilize both (S)-1,2-propanediol and (R)-1,2-propanediol as a substrate, with an observed preference for the S enantiomer. Based on the new structural information we developed and successfully tested a hypothesis that explains the functional differences we observe.
Highlights
In contrast to the well characterized B12-dependent dehydratases [1, 2], only one glycyl radical enzyme (GRE)2 or Glycyl radical enzymes (GREs)-type dehydratase has been characterized to date [3]
Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is a diol dehydratase
In contrast to the well characterized B12-dependent dehydratases [1, 2], only one glycyl radical enzyme (GRE)2 or GRE-type dehydratase has been characterized to date [3]
Summary
In contrast to the well characterized B12-dependent dehydratases [1, 2], only one glycyl radical enzyme (GRE) or GRE-type dehydratase has been characterized to date [3]. It is recognized that GREs can catalyze the formation of C-C bonds (benzyl succinate synthase) [11], C-C bond cleavage (PFL and 4-hydroxyphenylacetate decarboxylase) [5, 12], anaerobic ribonucleotide reduction [8], dehydration reactions (glycerol dehydratase) [3], and C-N bond cleavage (choline trimethylamine-lyase) [13,14,15] Taken together, these observations underscore a superfamily of enzymes that utilize a conserved structural core to perform vastly different radical-catalyzed reactions. In addition to the presence of the proposed GRE-type dehydratase gene, the operon containing the diol dehydratase (WP_007885173) contained another gene that was consistent with that of an “activating enzyme” (ABC25540) These observations are significant because all of the GREs that have been investigated to date are expressed in an inactive form that is post-translationally activated by an activating enzyme (AE).
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