8WP5

Crystal structure of LbUGT1 in complex with UDP

Summary for 8WP5

• Entry DOI: 10.2210/pdb8wp5/pdb
• Descriptor: Glycosyltransferase, URIDINE-5'-DIPHOSPHATE, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: lycibarbarspermidines, biosynthesis, glycosyltransferase, transferase
• Biological source: Lycium barbarum
• Total number of polymer chains: 1
• Total formula weight: 55412.28

Authors

Hu, D.,Wang, G.Q. (deposition date: 2023-10-08, release date: 2024-05-22, Last modification date: 2024-10-30)

Primary citation

Li, S.Y.,Wang, G.Q.,Long, L.,Gao, J.L.,Zhou, Z.Q.,Wang, Y.H.,Lv, J.M.,Chen, G.D.,Hu, D.,Abe, I.,Gao, H.
Functional and structural dissection of glycosyltransferases underlying the glycodiversity of wolfberry-derived bioactive ingredients lycibarbarspermidines.
Nat Commun, 15:4588-4588, 2024

PubMed Abstract: Lycibarbarspermidines are unusual phenolamide glycosides characterized by a dicaffeoylspermidine core with multiple glycosyl substitutions, and serve as a major class of bioactive ingredients in the wolfberry. So far, little is known about the enzymatic basis of the glycosylation of phenolamides including dicaffeoylspermidine. Here, we identify five lycibarbarspermidine glycosyltransferases, LbUGT1-5, which are the first phenolamide-type glycosyltransferases and catalyze regioselective glycosylation of dicaffeoylspermidines to form structurally diverse lycibarbarspermidines in wolfberry. Notably, LbUGT3 acts as a distinctive enzyme that catalyzes a tandem sugar transfer to the ortho-dihydroxy group on the caffeoyl moiety to form the unusual ortho-diglucosylated product, while LbUGT1 accurately discriminates caffeoyl and dihydrocaffeoyl groups to catalyze a site-selective sugar transfer. Crystal structure analysis of the complexes of LbUGT1 and LbUGT3 with UDP, combined with molecular dynamics simulations, revealed the structural basis of the difference in glycosylation selectivity between LbUGT1 and LbUGT3. Site-directed mutagenesis illuminates a conserved tyrosine residue (Y389 in LbUGT1 and Y390 in LbUGT3) in PSPG box that plays a crucial role in regulating the regioselectivity of LbUGT1 and LbUGT3. Our study thus sheds light on the enzymatic underpinnings of the chemical diversity of lycibarbarspermidines in wolfberry, and expands the repertoire of glycosyltransferases in nature.

PubMed: 38816433
DOI: 10.1038/s41467-024-49010-9

Experimental method

X-RAY DIFFRACTION (2.57005953651 Å)