6BTD

Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose

6BTD の概要

• エントリーDOI: 10.2210/pdb6btd/pdb
• 分子名称: Fuculose phosphate aldolase, SULFATE ION, MANGANESE (II) ION, ... (4 entities in total)
• 機能のキーワード: 5-deoxyribose, radical sam enzyme byproduct, aldolase, lyase
• 由来する生物種: Bacillus thuringiensis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 25094.34

構造登録者

Li, Q.,Bruner, S.D. (登録日: 2017-12-06, 公開日: 2018-07-04, 最終更新日: 2023-10-04)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.551 Å)