4ZU5

Crystal structure of the QdtA 3,4-Ketoisomerase from Thermoanaerobacterium thermosaccharolyticum, apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Bacterial Sugar 3,4-Ketoisomerases: Structural Insight into Product Stereochemistry.

Thoden, J.B.Vinogradov, E.Gilbert, M.Salinger, A.J.Holden, H.M.

(2015) Biochemistry 54: 4495-4506

  • DOI: 10.1021/acs.biochem.5b00541
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 3-Acetamido-3,6-dideoxy-d-galactose (Fuc3NAc) and 3-acetamido-3,6-dideoxy-d-glucose (Qui3NAc) are unusual sugars found on the lipopolysaccharides of Gram-negative bacteria and on the S-layers of Gram-positive bacteria. The 3,4-ketoisomerases, referre ...

    3-Acetamido-3,6-dideoxy-d-galactose (Fuc3NAc) and 3-acetamido-3,6-dideoxy-d-glucose (Qui3NAc) are unusual sugars found on the lipopolysaccharides of Gram-negative bacteria and on the S-layers of Gram-positive bacteria. The 3,4-ketoisomerases, referred to as FdtA and QdtA, catalyze the third steps in the respective biosynthetic pathways for these sugars. Whereas both enzymes utilize the same substrate, the stereochemistries of their products are different. Specifically, the hydroxyl groups at the hexose C-4' positions assume the "galactose" and "glucose" configurations in the FdtA and QdtA products, respectively. In 2007 we reported the structure of the apoform of FdtA from Aneurinibacillus thermoaerophilus, which was followed in 2014 by the X-ray analysis of QdtA from Thermoanaerobacterium thermosaccharolyticum as a binary complex. Both of these enzymes belong to the cupin superfamily. Here we report a combined structural and enzymological study to explore the manner in which these enzymes control the stereochemistry of their products. Various site-directed mutant proteins of each enzyme were constructed, and their dTDP-sugar products were analyzed by NMR spectroscopy. In addition, the kinetic parameters for these protein variants were measured, and the structure of one, namely, the QdtA Y17R/R97H double mutant form, was determined to 2.3-√Ö resolution. Finally, in an attempt to obtain a model of FdtA with a bound dTDP-linked sugar, the 3,4-ketoisomerase domain of a bifunctional enzyme from Shewanella denitrificans was cloned, purified, and crystallized in the presence of a dTDP-linked sugar analogue. Taken together, the results from this investigation demonstrate that it is possible to convert a "galacto" enzyme into a "gluco" enzyme and vice versa.


    Organizational Affiliation

    †Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
QdtA
A, B
144Thermoanaerobacterium thermosaccharolyticumMutation(s): 0 
Gene Names: qdtA
Find proteins for Q6TFC5 (Thermoanaerobacterium thermosaccharolyticum)
Go to UniProtKB:  Q6TFC5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PXN
Query on PXN

Download SDF File 
Download CCD File 
B
(2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol
PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)
C17 H36 O8
GXEZGLLPFFKHGE-FPCVCCKLSA-N
 Ligand Interaction
THM
Query on THM

Download SDF File 
Download CCD File 
A, B
THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.742α = 90.00
b = 93.742β = 90.00
c = 95.623γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
PHASERphasing
REFMACrefinement
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release