5-Deoxyribose is derived from 5’-deoxyadenosine, a toxic byproduct of all radical S-adenosylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown, but a salvage pathway is proposed to involve phosphorylation, isomerization, and a retro-aldol reaction. Analysis of bacterial genomes uncovered widespread, unassigned three-gene clusters specifying this predicted putative kinase, isomerase and aldolase. The enzymes encoded by the gene cluster from Bacillus thuringiensis, acting sequentially in vitro, converted 5-deoxyribose to dihydroxyacetone phosphate and acetaldehyde via 5-deoxyribose 1-phosphate and 5-deoxyribulose 1-phosphate. The aldolase is a unique member among class II aldolase family with an unusual manganese binding active site and aldehyde co-substrate. Our two structures of the aldolase, bound and unbound substrate, allow a scrutiny of mechanistic study and expand the utilization of chemoenzymatic tool to introduce chiral center. This work defines to our knowledge the first salvage pathway for 5-deoxyribose, an essentially universal metabolite.

Dispatching the ubiquitous radical SAM enzymes byproduct 5-deoxyribose

256th National Meeting (2018)

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