Structure determination of the TMP-complex of EvaD

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1074/jbc.M404091200
  • Primary Citation of Related Structures:  

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
205Amycolatopsis orientalisMutation(s): 0 
Find proteins for O52806 (Amycolatopsis orientalis)
Explore O52806 
Go to UniProtKB:  O52806
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO52806
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description