8JJN

Structure of SenB in complex with UDP-Glc and PO4- at 1.98 Angstroms resolution

8JJN の概要

• エントリーDOI: 10.2210/pdb8jjn/pdb
• 分子名称: TIGR04348 family glycosyltransferase, URIDINE-5'-DIPHOSPHATE-GLUCOSE, PHOSPHATE ION, ... (4 entities in total)
• 機能のキーワード: complex with udp-glc and po4-, transferase
• 由来する生物種: Variovorax paradoxus
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 107085.63

構造登録者

Huang, W.,Long, F. (登録日: 2023-05-31, 公開日: 2024-02-07, 最終更新日: 2025-08-20)

主引用文献

Huang, W.,Song, J.,Sun, T.,He, Y.,Li, X.,Deng, Z.,Long, F.
Substrate binding and catalytic mechanism of the Se-glycosyltransferase SenB in the biosynthesis of selenoneine.
Nat Commun, 15:1659-1659, 2024

PubMed Abstract: Selenium is an essential multifunctional trace element in diverse organisms. The only Se-glycosyltransferase identified that catalyzes the incorporation of selenium in selenoneine biosynthesis is SenB from Variovorax paradoxus. Although the biochemical function of SenB has been investigated, its substrate specificity, structure, and catalytic mechanism have not been elucidated. Here, we reveal that SenB exhibits sugar donor promiscuity and can utilize six UDP-sugars to generate selenosugars. We report crystal structures of SenB complexed with different UDP-sugars. The key elements N20/T23/E231 contribute to the sugar donor selectivity of SenB. A proposed catalytic mechanism is tested by structure-guided mutagenesis, revealing that SenB yields selenosugars by forming C-Se glycosidic bonds via spontaneous deprotonation and disrupting Se-P bonds by nucleophilic water attack, which is initiated by the critical residue K158. Furthermore, we functionally and structurally characterize two other Se-glycosyltransferases, CbSenB from Comamonadaceae bacterium and RsSenB from Ramlibacter sp., which also exhibit sugar donor promiscuity.

PubMed: 38395953
DOI: 10.1038/s41467-024-46065-6

実験手法

X-RAY DIFFRACTION (1.98 Å)