1OJ7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.jmb.2004.07.034
  • Primary Citation of Related Structures:  
    1OJ7

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOTHETICAL OXIDOREDUCTASE YQHD
A, B, C, D
408Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for Q46856 (Escherichia coli (strain K12))
Explore Q46856 
Go to UniProtKB:  Q46856
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46856
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NZQ
Query on NZQ

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
L [auth D]
5,6-DIHYDROXY-NADP
C21 H32 N7 O19 P3
LRAVAOPKUBJONV-IVCJQJMGSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth B],
I [auth C],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
BO3
Query on BO3

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 237.925α = 90
b = 237.925β = 90
c = 66.744γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
MLPHAREphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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