1E3J

Ketose reductase (sorbitol dehydrogenase) from silverleaf whitefly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Nadp(H)-Dependent Ketose Reductase from Besimia Argentifolii at 2.3 Angstrom Resolution

Banfield, M.J.Salvucci, M.E.Baker, E.N.Smith, C.A.

(2001) J Mol Biol 306: 239

  • DOI: 10.1006/jmbi.2000.4381
  • Primary Citation of Related Structures:  
    1E3J

  • PubMed Abstract: 
  • Polyhydric alcohols are widely found in nature and can be accumulated to high concentrations as a protection against a variety of environmental stresses. It is only recently, however, that these molecules have been shown to be active in protection ag ...

    Polyhydric alcohols are widely found in nature and can be accumulated to high concentrations as a protection against a variety of environmental stresses. It is only recently, however, that these molecules have been shown to be active in protection against heat stress, specifically in the use of sorbitol by the silverleaf whitefly, Bemisia argentifolii. We have determined the structure of the enzyme responsible for production of sorbitol in Bemisia argentifolii, NADP(H)-dependent ketose reductase (BaKR), to 2.3 A resolution. The structure was solved by multiwavelength anomalous diffraction (MAD) using the anomalous scattering from two zinc atoms bound in the structure, and was refined to an R factor of 21.9 % (R(free)=25.1 %). BaKR belongs to the medium-chain dehydrogenase family and its structure is the first for the sorbitol dehydrogenase branch of this family. The enzyme is tetrameric, with the monomer having a very similar fold to the alcohol dehydrogenases (ADHs). Although the structure determined is for the apo form, a phosphate ion in the active site marks the likely position for the adenyl phosphate of NADP(H). The catalytic zinc ion is tetrahedrally coordinated to Cys41, His66, Glu67 and a water molecule, in a modification of the zinc site usually found in ADHs. This modified zinc site seems likely to be a conserved feature of the sorbitol dehydrogenase sub-family. Comparisons with other members of the ADH family have also enabled us to model a ternary complex of the enzyme, and suggest how structural differences may influence coenzyme binding and substrate specificity in the reduction of fructose to sorbitol.


    Related Citations: 
    • Nadp-Dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Co-Factor-Binding and Co-Factor Specificity of the Adhs of Clostridium Beijerinckii and Thermoanaerobacter Brockii
      Korkhin, Y., Kalb, A.J., Peretz, M., Bogin, O., Burstein, Y., Frolow, F.
      (1998) J Mol Biol 278: 967
    • Nadp-Dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Co-Factor-Binding and Co-Factor Specificity of the Adhs of Clostridium Beijerinckii and Thermoanaerobacter Brockii
      Eklund, H., Nordstrom, B., Zeppezauer, E., Soderlund, G., Ohlsson, I., Boiwe, T., Soderberg, B.O., Tapia, O., Branden, C.I.
      (1976) J Mol Biol 102: 27

    Organizational Affiliation

    School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADP(H)-DEPENDENT KETOSE REDUCTASEA352Bemisia argentifoliiMutation(s): 0 
Gene Names: Kr
Find proteins for O96496 (Bemisia argentifolii)
Explore O96496 
Go to UniProtKB:  O96496
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BO3
Query on BO3

Download CCD File 
A
BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.822α = 90
b = 98.395β = 90
c = 120.924γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance