8JJT

Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution

Summary for 8JJT

• Entry DOI: 10.2210/pdb8jjt/pdb
• Descriptor: TIGR04348 family glycosyltransferase, URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE (3 entities in total)
• Functional Keywords: udp-glcnac, transferase
• Biological source: Variovorax paradoxus
• Total number of polymer chains: 3
• Total formula weight: 107797.89

Authors

Wei, H.,Feng, L. (deposition date: 2023-05-31, release date: 2024-02-07, Last modification date: 2025-08-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.88 Å)