Salvage of the 5-deoxyribose byproduct of radical SAM enzymes

Nat Commun. 2018 Aug 6;9(1):3105. doi: 10.1038/s41467-018-05589-4.


5-Deoxyribose is formed from 5'-deoxyadenosine, a toxic byproduct of radical S-adenosylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown. Here, we define a salvage pathway for 5-deoxyribose in bacteria, consisting of phosphorylation, isomerization, and aldol cleavage steps. Analysis of bacterial genomes uncovers widespread, unassigned three-gene clusters specifying a putative kinase, isomerase, and sugar phosphate aldolase. We show that the enzymes encoded by the Bacillus thuringiensis cluster, acting together in vitro, convert 5-deoxyribose successively to 5-deoxyribose 1-phosphate, 5-deoxyribulose 1-phosphate, and dihydroxyacetone phosphate plus acetaldehyde. Deleting the isomerase decreases the 5-deoxyribulose 1-phosphate pool size, and deleting either the isomerase or the aldolase increases susceptibility to 5-deoxyribose. The substrate preference of the aldolase is unique among family members, and the X-ray structure reveals an unusual manganese-dependent enzyme. This work defines a salvage pathway for 5-deoxyribose, a near-universal metabolite.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aldehyde-Lyases / chemistry
  • Aldehydes / chemistry
  • Bacillus thuringiensis / enzymology*
  • Biological Transport
  • Crystallography, X-Ray
  • Deoxyadenosines / chemistry
  • Deoxyribose / chemistry*
  • Escherichia coli / metabolism
  • Gene Deletion
  • Isomerases / chemistry
  • Metabolomics
  • Phenotype
  • Phosphotransferases / chemistry
  • Protein Conformation
  • Ribosemonophosphates / chemistry
  • S-Adenosylmethionine / chemistry*


  • Aldehydes
  • Deoxyadenosines
  • Ribosemonophosphates
  • 5'-deoxyadenosine
  • Deoxyribose
  • S-Adenosylmethionine
  • 5-deoxyribose 1-phosphate
  • 3-hydroxybutanal
  • Phosphotransferases
  • Aldehyde-Lyases
  • Isomerases