Crystal structure of the short chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD+ and 1,2-Pentandiol

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Structural Insight Into Substrate Differentiation of the Sugar-Metabolizing Enzyme Galactitol Dehydrogenase from Rhodobacter Sphaeroides D.

Carius, Y.Christian, H.Faust, A.Zander, U.Klink, B.U.Kornberger, P.Kohring, G.W.Giffhorn, F.Scheidig, A.J.

(2010) J Biol Chem 285: 20006

  • DOI: https://doi.org/10.1074/jbc.M110.113738
  • Primary Citation of Related Structures:  
    2WDZ, 2WSB, 3LQF

  • PubMed Abstract: 

    Galactitol 2-dehydrogenase (GatDH) belongs to the protein superfamily of short-chain dehydrogenases. As an enzyme capable of the stereo- and regioselective modification of carbohydrates, it exhibits a high potential for application in biotechnology as a biocatalyst. We have determined the crystal structure of the binary form of GatDH in complex with its cofactor NAD(H) and of the ternary form in complex with NAD(H) and three different substrates. The active form of GatDH constitutes a homo-tetramer with two magnesium-ion binding sites each formed by two opposing C termini. The catalytic tetrad is formed by Asn(116), Ser(144), Tyr(159), and Lys(163). GatDH structurally aligns well with related members of the short-chain dehydrogenase family. The substrate binding pocket can be divided into two parts of different size and polarity. In the smaller part, the side chains of amino acids Ser(144), Ser(146), and Asn(151) are important determinants for the binding specificity and the orientation of (pro-) chiral compounds. The larger part of the pocket is elongated and flanked by polar and non-polar residues, enabling a rather broad substrate spectrum. The presented structures provide valuable information for a rational design of this enzyme to improve its stability against pH, temperature, or solvent concentration and to optimize product yield in bioreactors.

  • Organizational Affiliation

    Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
254Cereibacter sphaeroidesMutation(s): 0 
Find proteins for C0KTJ6 (Cereibacter sphaeroides)
Explore C0KTJ6 
Go to UniProtKB:  C0KTJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0KTJ6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D]
C21 H27 N7 O14 P2
Query on 1SP

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B],
N [auth C],
Q [auth D]
C5 H12 O2
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.72α = 90
b = 113.62β = 90
c = 256.925γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description