6BTG

Crystal structure of deoxyribose-phosphate aldolase bound with DHAP from Bacillus Thuringiensis

Summary for 6BTG

• Entry DOI: 10.2210/pdb6btg/pdb
• Descriptor: Fuculose phosphate aldolase, MANGANESE (II) ION, 1,3-DIHYDROXYACETONEPHOSPHATE, ... (4 entities in total)
• Functional Keywords: dhap, 5-deoxyribose, radical sam enzyme byproduct, lyase
• Biological source: Bacillus thuringiensis
• Total number of polymer chains: 1
• Total formula weight: 25168.33

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

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: 30082730
DOI: 10.1038/s41467-018-05589-4

Experimental method

X-RAY DIFFRACTION (1.698 Å)