4JLW

Crystal structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb4JLW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa LESB58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-13 Released: 2013-10-30 
• Deposition Author(s): Chen, S., Liao, Y.P., Wang, D.L., Wang, S., Ding, J.F., Wang, Y.M., Cai, L.J., Ran, X.Y., Zhu, H.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

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 Struct Biol Cryst Commun 69: 967-972

• PubMed: 23989142 
• DOI: https://doi.org/10.1107/S174430911302160X
• Primary Citation of Related Structures:  
  4JLW


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 171.98 kDa 
• Atom Count: 12,372 
• Modelled Residue Count: 1,580 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione-independent formaldehyde dehydrogenase	A, B, C, D	399	Pseudomonas aeruginosa LESB58	Mutation(s): 0  Gene Names: fdhA, PLES_58161

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A], K [auth B], P [auth C], U [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	H [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], V [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A], I [auth B], J [auth B], N [auth C], O [auth C], S [auth D], T [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.226	α = 90
b = 98.305	β = 91.29
c = 99.623	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Chen, S., Liao, Y.P., Wang, D.L., Wang, S., Ding, J.F., Wang, Y.M., Cai, L.J., Ran, X.Y., Zhu, H.X.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description