1,2-Propanediol Dehydration in Roseburia inulinivorans

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.

A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans -4-hydroxy- l -proline

“…Our model and docking agree well with a recently reported crystal structure of PD bound to ( S )-1,2-propanediol (root-mean-square deviation of 0.56 Å) (Fig. S9) (39). Site-directed mutagenesis experiments confirmed that these four residues are critical for activity (Fig.…”

Bacterial microcompartments

“…The latter is used by a lactaldehyde reductase to produce 1,2-propanediol. This led to the assumption that the GRE of GRM5 was a 1,2-propanediol dehydratase, which was later experimentally verified 90 . This activity was then also proposed for the GREs that are associated with the GRM3 and GRM4; phylogenetic analyses showed that the GREs of GRM3 and GRM4 cluster closely together with the GREs of GRM5 in a maximum-likelihood tree [G] 8 .…”

New tricks for the glycyl radical enzyme family

“…Currently, this family consists of glycerol dehydratase (GDH) (O’Brien et al , 2004), propane-1,2-diol dehydratase (PDH) (LaMattina et al , 2016), and choline trimethylamine-lyase (CutC) (Craciun and Balskus, 2012). …”

“…This enzyme shares 48% sequence identity with GDH, but preferentially catalyzes the conversion of propane-1,2-diol into propanal (LaMattina et al , 2016) (Fig. 1).…”

“…The reactions catalyzed by GREs are diverse (Fig. 1) and are involved in metabolic pathways including mixed acid fermentation following glycolysis (Knappe and Wagner, 1995), DNA synthesis (Sun et al , 1996), and anaerobic metabolism of toluene (Leuthner et al , 1998), choline (Craciun and Balskus, 2012), tyrosine/4-hydroxyphenylacetate (Yu et al , 2006), glycerol (O’Brien et al , 2004), and propane-1,2-diol (LaMattina et al , 2016). Although glycyl radicals have the benefit of being simple, protein-based radical storage cofactors, they are extremely oxygen-sensitive.…”