1EZ0

CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE FROM VIBRIO HARVEYI.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the NADP+-dependent aldehyde dehydrogenase from Vibrio harveyi: structural implications for cofactor specificity and affinity.

Ahvazi, B.Coulombe, R.Delarge, M.Vedadi, M.Zhang, L.Meighen, E.Vrielink, A.

(2000) Biochem.J. 349: 853-861

  • Primary Citation of Related Structures:  1EYY

  • PubMed Abstract: 
  • Aldehyde dehydrogenase from the bioluminescent bacterium, Vibrio harveyi, catalyses the oxidation of long-chain aliphatic aldehydes to acids. The enzyme is unique compared with other forms of aldehyde dehydrogenase in that it exhibits a very high spe ...

    Aldehyde dehydrogenase from the bioluminescent bacterium, Vibrio harveyi, catalyses the oxidation of long-chain aliphatic aldehydes to acids. The enzyme is unique compared with other forms of aldehyde dehydrogenase in that it exhibits a very high specificity and affinity for the cofactor NADP(+). Structural studies of this enzyme and comparisons with other forms of aldehyde dehydrogenase provide the basis for understanding the molecular features that dictate these unique properties and will enhance our understanding of the mechanism of catalysis for this class of enzyme. The X-ray structure of aldehyde dehydrogenase from V. harveyi has been solved to 2.5-A resolution as a partial complex with the cofactor NADP(+) and to 2. 1-A resolution as a fully bound 'holo' complex. The cofactor preference exhibited by different forms of the enzyme is predominantly determined by the electrostatic environment surrounding the 2'-hydroxy or the 2'-phosphate groups of the adenosine ribose moiety of NAD(+) or NADP(+), respectively. In the NADP(+)-dependent structures the presence of a threonine and a lysine contribute to the cofactor specificity. In the V. harveyi enzyme an arginine residue (Arg-210) contributes to the high cofactor affinity through a pi stacking interaction with the adenine ring system of the cofactor. Further differences between the V. harveyi enzyme and other aldehyde dehydrogenases are seen in the active site, in particular a histidine residue which is structurally conserved with phosphorylating glyceraldehyde-3-phosphate dehydrogenase. This may suggest an alternative mechanism for activation of the reactive cysteine residue for nucleophilic attack.


    Related Citations: 
    • Crystallization and Preliminary X-ray Analysis of Aldehyde Dehydrogenase from Vibrio harveyi
      Croteau, N.,Vedadi, M.,Delarge, M.,Meighen, E.,Abu-Abed, M.,Howell, P.L.,Vrielink, A.
      (1996) Protein Sci. 5: 2130


    Organizational Affiliation

    Biochemistry Department, McIntyre Medical Sciences Building, McGill University, 3655 Drummond Street, Montréal, Québec, Canada H3G 1Y6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALDEHYDE DEHYDROGENASE
A, B, C, D
510Vibrio harveyiGene Names: aldH
EC: 1.2.1.4
Find proteins for Q56694 (Vibrio harveyi)
Go to UniProtKB:  Q56694
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.380α = 90.00
b = 131.180β = 92.49
c = 92.540γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-24
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations