2P6P

X-ray crystal structure of C-C bond-forming dTDP-D-Olivose-transferase UrdGT2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and action of the C-C bond-forming glycosyltransferase UrdGT2 involved in the biosynthesis of the antibiotic urdamycin.

Mittler, M.Bechthold, A.Schulz, G.E.

(2007) J.Mol.Biol. 372: 67-76

  • DOI: 10.1016/j.jmb.2007.06.005

  • PubMed Abstract: 
  • The glycosyltransferase UrdGT2 from Streptomyces fradiae catalyzes the formation of a glycosidic C-C bond between a polyketide aglycone and D-olivose. The enyzme was expressed in Escherichia coli, purified and crystallized. Its structure was establis ...

    The glycosyltransferase UrdGT2 from Streptomyces fradiae catalyzes the formation of a glycosidic C-C bond between a polyketide aglycone and D-olivose. The enyzme was expressed in Escherichia coli, purified and crystallized. Its structure was established by X-ray diffraction at 1.9 A resolution. It is the first structure of a C-glycosyltransferase. UrdGT2 belongs to the structural family GT-B of the glycosyltransferases and is likely to form a C(2)-symmetric dimer in solution. The binding structures of donor and acceptor substrates in five structurally homologous enzymes provided a clear and consistent guide for the substrate-binding structure in UrdGT2. The modeled substrate locations suggest the deeply buried Asp137 as the activator for C-C bond formation and explain the reaction. The putative model can be used to design mutations that change the substrate specificity. Such mutants are of great interest in overcoming the increasing danger of antibiotic resistance.


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg im Breisgau, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycosyl transferase
A, B
384Streptomyces fradiaeMutation(s): 0 
Gene Names: urdGT2
Find proteins for Q9RPA7 (Streptomyces fradiae)
Go to UniProtKB:  Q9RPA7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.872α = 90.00
b = 78.904β = 90.00
c = 133.958γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
SHARPphasing
SLS-X06SAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance