6BTD
Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose
Summary for 6BTD
| Entry DOI | 10.2210/pdb6btd/pdb |
| Descriptor | Fuculose phosphate aldolase, SULFATE ION, MANGANESE (II) ION, ... (4 entities in total) |
| Functional Keywords | 5-deoxyribose, radical sam enzyme byproduct, aldolase, lyase |
| Biological source | Bacillus thuringiensis |
| Total number of polymer chains | 1 |
| Total formula weight | 25094.34 |
| Authors | Li, Q.,Bruner, S.D. (deposition date: 2017-12-06, release date: 2018-07-04, Last modification date: 2023-10-04) |
| Primary citation | Beaudoin, G.A.W.,Li, Q.,Folz, J.,Fiehn, O.,Goodsell, J.L.,Angerhofer, A.,Bruner, S.D.,Hanson, A.D. Salvage of the 5-deoxyribose byproduct of radical SAM enzymes. Nat Commun, 9:3105-3105, 2018 Cited by PubMed Abstract: 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. PubMed: 30082730DOI: 10.1038/s41467-018-05589-4 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.551 Å) |
Structure validation
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