4JLW

Crystal structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa: the binary complex with the cofactor NAD+.

Liao, Y.P.Chen, S.Wang, D.L.Zhang, W.Wang, S.Ding, J.F.Wang, Y.M.Cai, L.J.Ran, X.Y.Wang, X.Zhu, H.X.

(2013) Acta Crystallogr.,Sect.F 69: 967-972

  • DOI: 10.1107/S174430911302160X

  • PubMed Abstract: 
  • Formaldehyde dehydrogenase (FDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family which oxidizes toxic formaldehyde to formate using NAD(+) as an electron carrier. Three-dimensional structures have been reported for FDHs f ...

    Formaldehyde dehydrogenase (FDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family which oxidizes toxic formaldehyde to formate using NAD(+) as an electron carrier. Three-dimensional structures have been reported for FDHs from several different species. Most FDHs are dependent on glutathione for catalysis, but the enzyme from Pseudomonas putida is an exception. In this structural communication, the recombinant production, crystallization and X-ray structure determination at 2.7 Å resolution of FDH from P. aeruginosa are described. Both the tetrameric assembly and the NAD(+)-binding mode of P. aeruginosa FDH are similar to those of P. putida FDH, which is in good agreement with the high sequence identity (87.97%) between these two proteins. Preliminary enzymatic kinetics studies of P. aeruginosa FDH also revealed a conserved glutathione-independent `ping-pong' mechanism of formaldehyde oxidization.


    Organizational Affiliation

    R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione-independent formaldehyde dehydrogenase
A, B, C, D
399N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.226α = 90.00
b = 98.305β = 91.29
c = 99.623γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
HKL-2000data collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release