1WND

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure and Kinetics Identify Escherichia coli YdcW Gene Product as a Medium-chain Aldehyde Dehydrogenase

Gruez, A.Roig-Zamboni, V.Grisel, S.Salomoni, A.Valencia, C.Campanacci, V.Tegoni, M.Cambillau, C.

(2004) J.Mol.Biol. 343: 29-41

  • DOI: 10.1016/j.jmb.2004.08.030
  • Primary Citation of Related Structures:  1WNB

  • PubMed Abstract: 
  • In the context of a medium-scaled structural genomics program aiming at solving the structures of as many as possible bacterial unknown open reading frame products from Escherichia coli (Y prefix), we have solved the structure of YdcW at 2.1A resolut ...

    In the context of a medium-scaled structural genomics program aiming at solving the structures of as many as possible bacterial unknown open reading frame products from Escherichia coli (Y prefix), we have solved the structure of YdcW at 2.1A resolution, using molecular replacement. According to its sequence identity, YdcW has been classified into the betaine aldehyde dehydrogenases family (EC 1.2.1.8), catalysing the oxidation of betaine aldehyde into glycine betaine. The structure of YdcW resembles that of other aldehyde dehydrogenases: it is tetrameric and binds a NADH molecule in each monomer. The NADH molecules, bound in the active site by soaking, are revealed to be in the "hydrolysis position". Activities experiments demonstrate that YdcW is more active on medium-chains aldehyde than on betaine aldehyde. However, soaking of betaine into YdcW crystals revealed its presence in one of the subunits, in two positions, a putative resting position and a hydride transfer ready position. Analysis of kinetics data and of the active site shape suggest an optimum binding of n-alkyl aldehydes up to seven to eight carbon atoms, possibly followed by a bulky cyclic or aromatic group.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, 31 chemin J. Aiguier, F-13402 Marseille Cedex 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative betaine aldehyde dehydrogenase
A, B, C, D
495Escherichia coli (strain K12)Gene Names: prr (ydcW)
EC: 1.2.1.19
Find proteins for P77674 (Escherichia coli (strain K12))
Go to UniProtKB:  P77674
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.036α = 90.00
b = 79.680β = 95.77
c = 158.669γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CCP4data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2016-12-28
    Type: Structure summary