1WNB

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 

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:  
    1WND, 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 resolution, using molecular replacement ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative betaine aldehyde dehydrogenaseA, B, C, D495Escherichia coli K-12Mutation(s): 0 
Gene Names: patDprrydcWb1444JW1439
EC: 1.2.1.8 (PDB Primary Data), 1.2.1.19 (UniProt), 1.2.1 (UniProt)
UniProt
Find proteins for P77674 (Escherichia coli (strain K12))
Explore P77674 
Go to UniProtKB:  P77674
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], H [auth C], I [auth D]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
BTL
Query on BTL

Download Ideal Coordinates CCD File 
F [auth B]BETAINE ALDEHYDE
C5 H12 N O
SXKNCCSPZDCRFD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.278α = 90
b = 168.895β = 90.65
c = 85.476γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2013-11-06
    Changes: Non-polymer description