3FRK

X-ray structure of QdtB from T. thermosaccharolyticum in complex with a PLP:TDP-3-aminoquinovose aldimine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose.

Thoden, J.B.Schaffer, C.Messner, P.Holden, H.M.

(2009) Biochemistry 48: 1553-1561

  • DOI: 10.1021/bi8022015

  • PubMed Abstract: 
  • 3-Acetamido-3,6-dideoxy-alpha-d-glucose or Quip3NAc is an unusual deoxyamino sugar found in the O-antigens of some Gram-negative bacteria and in the S-layers of Gram-positive bacteria. It is synthesized in these organisms as a dTDP-linked sugar via t ...

    3-Acetamido-3,6-dideoxy-alpha-d-glucose or Quip3NAc is an unusual deoxyamino sugar found in the O-antigens of some Gram-negative bacteria and in the S-layers of Gram-positive bacteria. It is synthesized in these organisms as a dTDP-linked sugar via the action of five enzymes. The focus of this investigation is on QdtB from Thermoanaerobacterium thermosaccharolyticum E207-71, a PLP-dependent aminotransferase that catalyzes the penultimate step in the production of dTDP-Quip3NAc. For this analysis, the enzyme was crystallized in the presence of its product, dTDP-Quip3N, and the structure was solved and refined to 2.15 A resolution. QdtB is a dimer, and its overall fold places it into the well-characterized aspartate aminotransferase superfamily. Electron density corresponding to the bound product reveals the presence of a Schiff base between C-4' of the PLP cofactor and the amino nitrogen of the sugar. Those amino acid side chains involved in binding the dTDP-sugar into the active site include Tyr 183, His 309, and Tyr 310 from subunit 1 and Lys 219 from subunit 2. Notably there is a decided lack of interactions between the pyranosyl C-4' hydroxyl of the dTDP-sugar and the protein. In keeping with this observation, we show that QdtB can also turn over dTDP-3-acetamido-3,6-dideoxy-alpha-d-galactose. This investigation represents the first structural analysis of a sugar-modifying aminotransferase with a bound product in its active site that functions at the C-3' rather than the C-4' position of the hexose.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
QdtB
A, B
373Thermoanaerobacterium thermosaccharolyticumMutation(s): 0 
Gene Names: qdtB
Find proteins for Q6TFC4 (Thermoanaerobacterium thermosaccharolyticum)
Go to UniProtKB:  Q6TFC4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TQP
Query on TQP

Download SDF File 
Download CCD File 
A, B
(2R,3R,4S,5S,6R)-3,5-dihydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C24 H35 N4 O19 P3
UJDWKFAFGYHSFM-HMSDFHDVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 109.100α = 90.00
b = 109.100β = 90.00
c = 177.900γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance