1ZEM

Crystal Structure of NAD+-Bound Xylitol Dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity.

Ehrensberger, A.H.Elling, R.A.Wilson, D.K.

(2006) Structure 14: 567-575

  • DOI: 10.1016/j.str.2005.11.016

  • PubMed Abstract: 
  • Xylitol dehydrogenase (XDH) is one of several enzymes responsible for assimilating xylose into eukaryotic metabolism and is useful for fermentation of xylose contained in agricultural byproducts to produce ethanol. For efficient xylose utilization at ...

    Xylitol dehydrogenase (XDH) is one of several enzymes responsible for assimilating xylose into eukaryotic metabolism and is useful for fermentation of xylose contained in agricultural byproducts to produce ethanol. For efficient xylose utilization at high flux rates, cosubstrates should be recycled between the NAD+-specific XDH and the NADPH-preferring xylose reductase, another enzyme in the pathway. To understand and alter the cosubstrate specificity of XDH, we determined the crystal structure of the Gluconobacter oxydans holoenzyme to 1.9 angstroms resolution. The structure reveals that NAD+ specificity is largely conferred by Asp38, which interacts with the hydroxyls of the adenosine ribose. Met39 stacked under the purine ring and was also located near the 2' hydroxyl. Based on the location of these residues and on sequence alignments with related enzymes of various cosubstrate specificities, we constructed a double mutant (D38S/M39R) that was able to exclusively use NADP+, with no loss of activity.


    Organizational Affiliation

    Section of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
xylitol dehydrogenase
A, B, C, D, E, F, G, H
262Gluconobacter oxydansMutation(s): 0 
Gene Names: xdh
Find proteins for Q8GR61 (Gluconobacter oxydans)
Go to UniProtKB:  Q8GR61
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.959α = 90.00
b = 64.717β = 93.06
c = 168.239γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
EPMRphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance