Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP-L-rhamnose

Experimental Data Snapshot

  • Resolution: 3.21 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

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Crystal structures of rhamnosyltransferase UGT89C1 from Arabidopsis thaliana reveal the molecular basis of sugar donor specificity for UDP-beta-l-rhamnose and rhamnosylation mechanism.

Zong, G.Fei, S.Liu, X.Li, J.Gao, Y.Yang, X.Wang, X.Shen, Y.

(2019) Plant J 99: 257-269

  • DOI: https://doi.org/10.1111/tpj.14321
  • Primary Citation of Related Structures:  
    6IJ7, 6IJA, 6IJD

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-glycosyltransferase 89C1
A, B, C, D
435Arabidopsis thalianaMutation(s): 0 
Gene Names: UGT89C1
EC: 2.4.1
Find proteins for Q9LNE6 (Arabidopsis thaliana)
Explore Q9LNE6 
Go to UniProtKB:  Q9LNE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LNE6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AWU

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate
C15 H24 N2 O16 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.21 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.671α = 90
b = 84.983β = 89.92
c = 125.472γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina2017YFA0504801

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description