5TME

Crystal structure of Os79 from O. sativa in complex with UDP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Crystal Structure of Os79 (Os04g0206600) from Oryza sativa: A UDP-glucosyltransferase Involved in the Detoxification of Deoxynivalenol.

Wetterhorn, K.M.Newmister, S.A.Caniza, R.K.Busman, M.McCormick, S.P.Berthiller, F.Adam, G.Rayment, I.

(2016) Biochemistry 55: 6175-6186

  • DOI: https://doi.org/10.1021/acs.biochem.6b00709
  • Primary Citation of Related Structures:  
    5TMB, 5TMD, 5TME

  • PubMed Abstract: 

    Fusarium head blight is a plant disease with significant agricultural and health impact which affects cereal crops such as wheat, barley, and maize and is characterized by reduced grain yield and the accumulation of trichothecene mycotoxins such as deoxynivalenol (DON). Studies have identified trichothecene production as a virulence factor in Fusarium graminearum and have linked DON resistance to the ability to form DON-3-O-glucoside in wheat. Here, the structures of a deoxynivalenol:UDP-glucosyltransferase (Os79) from Oryza sativa are reported in complex with UDP in an open conformation, in complex with UDP in a closed conformation, and in complex with UDP-2-fluoro-2-deoxy-d-glucose and trichothecene at 1.8, 2.3, and 2.2 Å resolution, respectively. The active site of Os79 lies in a groove between the N-terminal acceptor and the C-terminal donor-binding domains. Structural alignments reveal that Os79 likely utilizes a catalytic mechanism similar to those of other plant UGTs, with His 27 activating the trichothecene O3 hydroxyl for nucleophilic attack at C1' of the UDP-glucose donor. Kinetic analysis of mutant Os79 revealed that Thr 291 plays a critical role in catalysis as a catalytic acid or to position the UDP moiety during the nucleophilic attack. Steady-state kinetic analysis demonstrated that Os79 conjugates multiple trichothecene substrates such as DON, nivalenol, isotrichodermol, and HT-2 toxin, but not T-2 toxin. These data establish a foundation for understanding substrate specificity and activity in this enzyme and can be used to guide future efforts to increase DON resistance in cereal crops.


  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyltransferase, Os79467Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os04g0206600OSJNBa0052O21.15OSNPB_040206600
EC: 2.4.1
UniProt
Find proteins for Q7XT97 (Oryza sativa subsp. japonica)
Explore Q7XT97 
Go to UniProtKB:  Q7XT97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7XT97
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.067α = 90
b = 83.306β = 90
c = 98.249γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institute of Food and Agriculture (NIFA, United States)United States1006542
United States Department of Agriculture (USDA)United States59-0206-1-117
Department of Energy (DOE, United States)United StatesW-31-109-ENG-38
Vienna Science and Technolgy FundAustriaLS12-021
Austrian Science Fund FWFAustriaSFB Fusarium

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2022-03-16
    Changes: Author supporting evidence, Database references
  • Version 1.6: 2024-11-20
    Changes: Data collection, Structure summary