2H6E

Crystal structure of the D-arabinose dehydrogenase from Sulfolobus solfataricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Crystal Structure and Biochemical Properties of the d-Arabinose Dehydrogenase from Sulfolobus solfataricus

Brouns, S.J.Turnbull, A.P.Willemen, H.L.Akerboom, J.van der Oost, J.

(2007) J.Mol.Biol. 371: 1249-1260

  • DOI: 10.1016/j.jmb.2007.05.097

  • PubMed Abstract: 
  • Sulfolobus solfataricus metabolizes the five-carbon sugar d-arabinose to 2-oxoglutarate by an inducible pathway consisting of dehydrogenases and dehydratases. Here we report the crystal structure and biochemical properties of the first enzyme of this ...

    Sulfolobus solfataricus metabolizes the five-carbon sugar d-arabinose to 2-oxoglutarate by an inducible pathway consisting of dehydrogenases and dehydratases. Here we report the crystal structure and biochemical properties of the first enzyme of this pathway: the d-arabinose dehydrogenase. The AraDH structure was solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure revealed a catalytic and cofactor binding domain, typically present in mesophilic and thermophilic alcohol dehydrogenases. Cofactor modeling showed the presence of a phosphate binding pocket sequence motif (SRS-X2-H), which is likely to be responsible for the enzyme's preference for NADP+. The homo-tetrameric enzyme is specific for d-arabinose, l-fucose, l-galactose and d-ribose, which could be explained by the hydrogen bonding patterns of the C3 and C4 hydroxyl groups observed in substrate docking simulations. The enzyme optimally converts sugars at pH 8.2 and 91 degrees C, and displays a half-life of 42 and 26 min at 85 and 90 degrees C, respectively, indicating that the enzyme is thermostable at physiological operating temperatures of 80 degrees C. The structure represents the first crystal structure of an NADP+-dependent member of the medium-chain dehydrogenase/reductase (MDR) superfamily from Archaea.


    Organizational Affiliation

    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, Netherlands. stan.brouns@wur.nl




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-arabinose 1-dehydrogenase
A
344Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: adh-4
EC: 1.1.1.1
Find proteins for Q97YM2 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97YM2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 84.019α = 90.00
b = 84.019β = 90.00
c = 194.979γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MAR345dtbdata collection
REFMACrefinement
SOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2014-11-12
    Type: Structure summary
  • Version 1.4: 2017-10-18
    Type: Refinement description
  • Version 1.5: 2018-01-24
    Type: Structure summary