1OFN

Purification, crystallisation and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis; the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Purification, Crystallization and Preliminary Structural Studies of Dtdp-4-Keto-6-Deoxy-Glucose-5-Epimerase (Evad) from Amycolatopsis Orientalis, the Fourth Enzyme in the Dtdp-L-Epivancosamine Biosynthetic Pathway.

Merkel, A.B.Temple, G.K.Burkart, M.D.Losey, H.C.Beis, K.Walsh, C.T.Naismith, J.H.

(2002) Acta Crystallogr.,Sect.D 58: 1226

  • Also Cited By: 1OI6

  • PubMed Abstract: 
  • The vancomycin class of antibiotics is regarded as the last line of defence against Gram-positive bacteria. The compounds used clinically are very complex organic molecules and are made by fermentation. The biosynthesis of these is complex and fascin ...

    The vancomycin class of antibiotics is regarded as the last line of defence against Gram-positive bacteria. The compounds used clinically are very complex organic molecules and are made by fermentation. The biosynthesis of these is complex and fascinating. Its study holds out the prospect of utilizing genetic engineering of the enzymes in the pathway in order to produce novel vancomycin analogues. In part, this requires detailed structural insight into substrate specificity as well as the enzyme mechanism. The crystallization of one of the enzymes in the chloroeremomycin biosynthetic pathway (a member of the vancomycin family), dTDP-3-amino-4-keto 2,3,6-trideoxy-3-C-methyl-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis, is reported here. The protein is fourth in the pathway which makes a carbohydrate essential for the activity of chloroeremomycin. The crystals of EvaD diffract to 1.5 A and have unit-cell parameters a = 98.6, b = 72.0, c = 57.1 A with space group P2(1)2(1)2. Data to this resolution were collected at the European Synchrotron Radiation Facility.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PCZA361.16
A, B
205Amycolatopsis orientalisN/A
Find proteins for O52806 (Amycolatopsis orientalis)
Go to UniProtKB:  O52806
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: 1.5 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.575α = 90.00
b = 71.996β = 90.00
c = 57.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MOSFLMdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance