1OJ7

STRUCTURAL GENOMICS, UNKNOWN FUNCTION CRYSTAL STRUCTURE OF E. COLI K-12 YQHD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of E.Coli Alcohol Dehydrogenase Yqhd: Evidence of a Covalently Modified Nadp Coenzyme

Sulzenbacher, G.Alvarez, K.Van-Den-Heuvel, R.H.H.Versluis, C.Spinelli, S.Campanacci, V.Valencia, C.Cambillau, C.Eklund, H.Tegoni, M.

(2004) J.Mol.Biol. 342: 489

  • DOI: 10.1016/j.jmb.2004.07.034

  • PubMed Abstract: 
  • In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame (ORF) products of unknown function, we have determined the structure of YqhD at 2.0A resolution using the single wavelength anomalo ...

    In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame (ORF) products of unknown function, we have determined the structure of YqhD at 2.0A resolution using the single wavelength anomalous diffraction method at the Pt edge. The crystal structure of YqhD reveals that it is an NADP-dependent dehydrogenase, a result confirmed by activity measurements with several alcohols. The current interpretation of our findings is that YqhD is an alcohol dehydrogenase (ADH) with preference for alcohols longer than C(3). YqhD is a dimer of 2x387 residues, each monomer being composed of two domains, a Rossmann-type fold and an alpha-helical domain. The crystals contain two dimers in the asymmetric unit. While one of the dimers contains a cofactor in both subunits, only one of the subunits in the second dimer contains it, making it possible to compare bound and unbound active sites. The active site contains a Zn atom, as verified by EXAFS on the crystals. The electron density maps of NADP revealed modifications of the nicotinamide ring by oxygen atoms at positions 5 and 6. Further analysis by electrospray mass spectrometry and comparison with the mass spectra of NADP and NADPH revealed the nature of the modification and the incorporation of two hydroxyl moieties at the 5 and 6 position in the nicotinamide ring, yielding NADPH(OH)(2). These modifications might be due to oxygen stress on an enzyme, which would functionally work under anaerobic conditions.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités d'Aix-Marseille I and II, 31 chemin J. Aiguier, F-13402 Marseille Cedex 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL OXIDOREDUCTASE YQHD
A, B, C, D
408Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yqhD
EC: 1.1.1.-
Find proteins for Q46856 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46856
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BO3
Query on BO3

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Download CCD File 
A, C
BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
 Ligand Interaction
NZQ
Query on NZQ

Download SDF File 
Download CCD File 
A, B, D
5,6-DIHYDROXY-NADP
C21 H32 N7 O19 P3
LRAVAOPKUBJONV-IVCJQJMGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.145 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 237.925α = 90.00
b = 237.925β = 90.00
c = 66.744γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
MLPHAREphasing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance