Substrate binding and catalytic mechanism of the Se-glycosyltransferase SenB in the biosynthesis of selenoneine

Wei Huang, Jun Song, Tianxue Sun, Yue He, Xiang Li, Zixin Deng and Feng Long ()
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Wei Huang: Wuhan University
Jun Song: Wuhan University
Tianxue Sun: Wuhan University
Yue He: Wuhan University
Xiang Li: Wuhan University
Zixin Deng: Wuhan University
Feng Long: Wuhan University

Nature Communications, 2024, vol. 15, issue 1, 1-10

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-46065-6

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