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Summary: Glycosylation is a key modification for most molecules including plant natural products, for example, flavonoids and isoflavonoids, and can enhance the bioactivity and bioavailability of the natural products. The crystal structure of plant rhamnosyltransferase UGT89C1 from Arabidopsis thaliana was determined, and the structures of UGT89C1 in complexes with UDP‐β‐l‐rhamnose and acceptor quercetin revealed the detailed interactions between the enzyme and its substrates. Structural and mutational analysis indicated that Asp356, His357, Pro147 and Ile148 are key residues for sugar donor recognition and specificity for UDP‐β‐l‐rhamnose. The mutant H357Q exhibited activity with both UDP‐β‐l‐rhamnose and UDP‐glucose. Structural comparison and mutagenesis confirmed that His21 is a key residue as the catalytic base and the only catalytic residue involved in catalysis independently as UGT89C1 lacks the other catalytic Asp that is highly conserved in other reported UGTs and forms a hydrogen bond with the catalytic base His. Ser124 is located in the corresponding position of the catalytic Asp in other UGTs and is not able to form a hydrogen bond with His21. Mutagenesis further showed that Ser124 may not be important in its catalysis, suggesting that His21 and acceptor may form an acceptor‐His dyad and UGT89C1 utilizes a catalytic dyad in catalysis instead of catalytic triad. The information of structure and mutagenesis provides structural insights into rhamnosyltransferase substrate specificity and rhamnosylation mechanism. Significance Statement: The crystal structures of plant rhamnosyltransferase UGT89C1 from Arabidopsis thaliana revealed the key structural features and residues for sugar donor recognition and specificity for UDP‐β‐l‐rhamnose. UGT89C1 utilizes His21 as the only catalytic residue for its catalysis as it lacks the other catalytic residue Asp, which is highly conserved in other reported UGTs, suggesting that His21 forms a catalytic dyad with acceptor to facilitate the UGT89C1‐mediated rhamnosylation. [ABSTRACT FROM AUTHOR]

Abstract The uridine diphosphate glycosyltransferase (UGT) plays the central role in glycosylation of small molecules by transferring sugars to various acceptors including bioactive natural products in plants. UGT89C1 from Arabidopsis thaliana is a novel UGT, a rhamnosyltransferase, specifically recognizes UDP- l -rhamnose as donor. To provide an insight into the sugar specificity for UDP- l -rhamnose and interactions between UGT89C1 and its substrates, the UGT89C1 was expressed in Escherichia coli and purified toward biochemical and structural studies. Enzyme activity assay was performed, and the recombinant UGT89C1 recognized UDP- l -rhamnose and rhamnosylated kaempferol. Crystals of At UGT89C1 were obtained, they diffracted to 2.7 Å resolution and belonged to space group I 4 1. At UGT89C1 was also co-crystallized with UDP. Interestingly, two crystal forms were obtained in the same crystallization condition, including the previous I 4 1 crystal form, and the new crystal form that diffracted to 3.0 Å resolution and belonged to space group P 2 1. Highlights • Expression in Escherichia coli and purification of the recombinant UGT89C1 have been established. • The recombinant UGT89C1 specifically recognized UDP- l -rhamnose and rhamnosylated kaempferol. • UGT89C1 was crystallized without and with UDP, and two crystal forms were obtained with UDP. • The X-ray crystallographic analysis of UGT89C1 was performed and discussed. [ABSTRACT FROM AUTHOR]