9KSW

Complex structure of CaApiGT/UMP/Rutin

Summary for 9KSW

• Entry DOI: 10.2210/pdb9ksw/pdb
• Descriptor: UDP-glycosyltransferase 79B30-like, URIDINE-5'-MONOPHOSPHATE, RUTIN, ... (4 entities in total)
• Functional Keywords: glycosyltransferase, apiosyltransferase, plant protein
• Biological source: Cicer arietinum (chickpea)
• Total number of polymer chains: 1
• Total formula weight: 52489.04

Authors

Wang, H.T.,Wang, Z.L.,Ye, M. (deposition date: 2024-11-30, release date: 2025-06-25, Last modification date: 2025-07-02)

Primary citation

Wang, H.T.,Wang, Z.L.,Chen, N.H.,Huang, W.,Zou, J.L.,Tian, Y.G.,Ye, G.,Huang, J.,Wu, R.,Ye, M.
Insights into the Mechanisms of Sugar Acceptor Selectivity of Plant Flavonoid Apiosyltransferases.
J.Am.Chem.Soc., 147:20631-20643, 2025

PubMed Abstract: Flavonoid apiosides are widely distributed in cereals, fruits, vegetables, and medicinal herbs and play critical roles in human health. Their facile and efficient synthesis has been a hot but challenging topic in the fields of both organic chemistry and biosynthesis. However, very few apiosyltransferases (ApiGTs) have been reported thus far. Here, we report the first flavonoid apiosyltransferase (CaApiGT) capable of catalyzing the 2″--apiosylation of flavonoid 3--glycosides in chickpea (). Moreover, we identify PcApiGT from parsley (), which catalyzes the 2″--apiosylation of flavonoid 7-/4'--glycosides. To dissect the mechanisms underlying their different sugar acceptor selectivity, we obtain 10 complex crystal structures of CaApiGT and PcApiGT with resolutions ranging from 1.55 to 2.65 Å, including CaApiGT/UDP, 6 ternary structures of CaApiGT/UDP/sugar acceptors, PcApiGT/UDP, and 2 ternary structures of PcApiGT/UDP/sugar acceptors. Structural analyses, theoretical calculations, and site-directed mutagenesis indicate that flavonoid 3--glycosides and 7--glycosides exhibit a T-shape and streamline shape, respectively, and fit the active pockets of CaApiGT and PcApiGT. Moreover, the sugar acceptor selectivity of these two apiosyltransferases is determined by a key α-helix. In CaApiGT, this α-helix contains multiple polar amino acids, particularly a threonine residue at its end. Using this α-helix motif as a marker, we further characterize four apiosyltransferases from Leguminosae plants that exhibit functional similarity to CaApiGT. This work unravels detailed sugar acceptor selectivity mechanisms of plant apiosyltransferases and provides efficient biocatalysts for the synthesis of flavonoid apiosides.

PubMed: 40459876
DOI: 10.1021/jacs.5c03771

Experimental method

X-RAY DIFFRACTION (2.05 Å)