1OI6

Structure determination of the TMP-complex of EvaD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Position of a Key Tyrosine in Dtdp-4-Keto-6-Deoxy-D-Glucose-5-Epimerase (Evad) Alters the Substrate Profile for This Rmlc-Like Enzyme

Merkel, A.B.Major, L.L.Errey, J.C.Burkart, M.D.Field, R.A.Walsh, C.T.Naismith, J.H.

(2004) J Biol Chem 279: 32684

  • DOI: 10.1074/jbc.M404091200
  • Primary Citation of Related Structures:  
    1OI6

  • PubMed Abstract: 
  • Vancomycin, the last line of defense antibiotic, depends upon the attachment of the carbohydrate vancosamine to an aglycone skeleton for antibacterial activity. Vancomycin is a naturally occurring secondary metabolite that can be produced by bacteria ...

    Vancomycin, the last line of defense antibiotic, depends upon the attachment of the carbohydrate vancosamine to an aglycone skeleton for antibacterial activity. Vancomycin is a naturally occurring secondary metabolite that can be produced by bacterial fermentation. To combat emerging resistance, it has been proposed to genetically engineer bacteria to produce analogues of vancomycin. This requires a detailed understanding of the biochemical steps in the synthesis of vancomycin. Here we report the 1.4 A structure and biochemical characterization of EvaD, an RmlC-like protein that is required for the C-5' epimerization during synthesis of dTDP-epivancosamine. EvaD, although clearly belonging to the RmlC class of enzymes, displays very low activity in the archetypal RmlC reaction (double epimerization of dTDP-6-deoxy-4-keto-D-glucose at C-3' and C-5'). The high resolution structure of EvaD compared with the structures of authentic RmlC enzymes indicates that a subtle change in the enzyme active site repositions a key catalytic Tyr residue. A mutant designed to re-establish the normal position of the Tyr increases the RmlC-like activity of EvaD.


    Related Citations: 
    • Purification, Crystallisation and Preliminary Structural Studies of Dtdp-4-Keto-6-Deoxy-Glucose-5-Epimerase (Evad) from Amycolatpsis Orientalis; the Fourth Enzyme in the Dtdp-L-Epivancosamine Pathway
      Merkel, A.B., Temple, G.K., Burkhart, M., Beis, K., Walsh, C.T., Naismith, J.H.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1226

    Organizational Affiliation

    Centre for Biomolecular Sciences, The University, St. Andrews, Scotland, KY16 9ST, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PCZA361.16A, B205Amycolatopsis orientalisMutation(s): 0 
Find proteins for O52806 (Amycolatopsis orientalis)
Explore O52806 
Go to UniProtKB:  O52806
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMP
Query on TMP

Download CCD File 
A, B
THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.5α = 90
b = 72.571β = 90
c = 57.239γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other