8FBX

Selenosugar synthase SenB from Variovorax paradoxus

Summary for 8FBX

• Entry DOI: 10.2210/pdb8fbx/pdb
• Descriptor: Selenosugar synthase SenB, SODIUM ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: se-c, biosynthesis, transferase
• Biological source: Variovorax paradoxus
• Total number of polymer chains: 3
• Total formula weight: 112606.79

Authors

Ireland, K.A.,Davis, K.M. (deposition date: 2022-11-30, release date: 2023-11-22, Last modification date: 2024-10-16)

Primary citation

Ireland, K.A.,Kayrouz, C.M.,Huang, J.,Seyedsayamdost, M.R.,Davis, K.M.
Structural Characterization and Ligand-Induced Conformational Changes of SenB, a Se-Glycosyltransferase Involved in Selenoneine Biosynthesis.
Biochemistry, 62:3337-3342, 2023

PubMed Abstract: Selenium (Se) is an essential micronutrient that is found naturally in proteins, nucleic acids, and natural products. Unlike selenoproteins and selenonucleic acids, little is known about the structures of biosynthetic enzymes that incorporate Se into small molecules. Here, we report the X-ray crystal structure of SenB, the first known Se-glycosyltransferase that was recently found to be involved in the biosynthesis of the Se-containing metabolite selenoneine. SenB catalyzes C-Se bond formation using selenophosphate and an activated uridine diphosphate sugar as a Se and glycosyl donor, respectively, making it the first known selenosugar synthase and one of only four C-Se bond-forming enzymes discovered to date. Our crystal structure, determined to 2.25 Å resolution, reveals that SenB is a type B glycosyltransferase, displaying the prototypical fold with two globular Rossmann-like domains and a catalytic interdomain cleft. By employing complementary structural biology techniques, we find that SenB undergoes both local and global substrate-induced conformational changes, demonstrating a significant increase in α-helicity and a transition to a more compact conformation. Our results provide the first structure of SenB and set the stage for further biochemical characterization in the future.

PubMed: 37966244
DOI: 10.1021/acs.biochem.3c00452

Experimental method

X-RAY DIFFRACTION (2.25 Å)