2VCE

Characterization and engineering of the bifunctional N- and O- glucosyltransferase involved in xenobiotic metabolism in plants


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization and Engineering of the Bifunctional N- and O-Glucosyltransferase Involved in Xenobiotic Metabolism in Plants.

Brazier-Hicks, M.Offen, W.A.Gershater, M.C.Revett, T.J.Lim, E.K.Bowles, D.J.Davies, G.J.Edwards, R.

(2007) Proc Natl Acad Sci U S A 104: 20238

  • DOI: 10.1073/pnas.0706421104
  • Primary Citation of Related Structures:  
    2VCE, 2VCH, 2VG8

  • PubMed Abstract: 
  • The glucosylation of pollutant and pesticide metabolites in plants controls their bioactivity and the formation of subsequent chemical residues. The model plant Arabidopsis thaliana contains >100 glycosyltransferases (GTs) dedicated to small-molecule conjugation and, whereas 44 of these enzymes catalyze the O-glucosylation of chlorinated phenols, only one, UGT72B1, shows appreciable N-glucosylating activity toward chloroanilines ...

    The glucosylation of pollutant and pesticide metabolites in plants controls their bioactivity and the formation of subsequent chemical residues. The model plant Arabidopsis thaliana contains >100 glycosyltransferases (GTs) dedicated to small-molecule conjugation and, whereas 44 of these enzymes catalyze the O-glucosylation of chlorinated phenols, only one, UGT72B1, shows appreciable N-glucosylating activity toward chloroanilines. UGT72B1 is a bifunctional O-glucosyltransferase (OGT) and N-glucosyltransferase (NGT). To investigate this unique dual activity, the structure of the protein was solved, at resolutions up to 1.45 A, in various forms including the Michaelis complex with intact donor analog and trichlorophenol acceptor. The catalytic mechanism and basis for O/N specificity was probed by mutagenesis and domain shuffling with an orthologous enzyme from Brassica napus (BnUGT), which possesses only OGT activity. Mutation of BnUGT at just two positions (D312N and F315Y) installed high levels of NGT activity. Molecular modeling revealed the connectivity of these residues to H19 on UGT72B1, with its mutagenesis exclusively defining NGT activity in the Arabidopsis enzyme. These results shed light on the conjugation of nonnatural substrates by plant GTs, highlighting the catalytic plasticity of this enzyme class and the ability to engineer unusual and desirable transfer to nitrogen-based acceptors.


    Organizational Affiliation

    Centre for Bioactive Chemistry, Durham University, Durham DH1 3LE, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROQUINONE GLUCOSYLTRANSFERASEA480Arabidopsis thalianaMutation(s): 0 
Gene Names: UGT72B1At4g01070F2N1.15
EC: 2.4.1.218 (PDB Primary Data), 2.4.1 (UniProt)
UniProt
Find proteins for Q9M156 (Arabidopsis thaliana)
Explore Q9M156 
Go to UniProtKB:  Q9M156
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U2F (Subject of Investigation/LOI)
Query on U2F

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-NQQHDEILSA-N
 Ligand Interaction
TC7 (Subject of Investigation/LOI)
Query on TC7

Download Ideal Coordinates CCD File 
C [auth A]2,4,5-trichlorophenol
C6 H3 Cl3 O
LHJGJYXLEPZJPM-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.807α = 90
b = 94.335β = 110.31
c = 57.059γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance