4JZ6

Crystal structure of a salicylaldehyde dehydrogenase from Pseudomonas putida G7 complexed with salicylaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.417 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation.

Coitinho, J.B.Pereira, M.S.Costa, D.M.Guimaraes, S.L.Araujo, S.S.Hengge, A.C.Brandao, T.A.Nagem, R.A.

(2016) Biochemistry 55: 5453-5463

  • DOI: 10.1021/acs.biochem.6b00614

  • PubMed Abstract: 
  • The salicylaldehyde dehydrogenase (NahF) catalyzes the oxidation of salicylaldehyde to salicylate using NAD(+) as a cofactor, the last reaction of the upper degradation pathway of naphthalene in Pseudomonas putida G7. The naphthalene is an abundant a ...

    The salicylaldehyde dehydrogenase (NahF) catalyzes the oxidation of salicylaldehyde to salicylate using NAD(+) as a cofactor, the last reaction of the upper degradation pathway of naphthalene in Pseudomonas putida G7. The naphthalene is an abundant and toxic compound in oil and has been used as a model for bioremediation studies. The steady-state kinetic parameters for oxidation of aliphatic or aromatic aldehydes catalyzed by 6xHis-NahF are presented. The 6xHis-NahF catalyzes the oxidation of aromatic aldehydes with large kcat/Km values close to 10(6) M(-1) s(-1). The active site of NahF is highly hydrophobic, and the enzyme shows higher specificity for less polar substrates than for polar substrates, e.g., acetaldehyde. The enzyme shows α/β folding with three well-defined domains: the oligomerization domain, which is responsible for the interlacement between the two monomers; the Rossmann-like fold domain, essential for nucleotide binding; and the catalytic domain. A salicylaldehyde molecule was observed in a deep pocket in the crystal structure of NahF where the catalytic C284 and E250 are present. Moreover, the residues G150, R157, W96, F99, F274, F279, and Y446 were thought to be important for catalysis and specificity for aromatic aldehydes. Understanding the molecular features responsible for NahF activity allows for comparisons with other aldehyde dehydrogenases and, together with structural information, provides the information needed for future mutational studies aimed to enhance its stability and specificity and further its use in biotechnological processes.


    Related Citations: 
    • Expression, purification and preliminary crystallographic studies of NahF, a salicylaldehyde dehydrogenase from Pseudomonas putida G7 involved in naphthalene degradation.
      Coitinho, J.B.,Costa, D.M.,Guimaraes, S.L.,de Goes, A.M.,Nagem, R.A.
      (2012) Acta Crystallogr.,Sect.F 68: 93


    Organizational Affiliation

    Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais , Belo Horizonte, MG 31270-901, Brazil.,Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte, MG 31270-901, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Salicylaldehyde dehydrogenase NahF
A
500Pseudomonas putidaMutation(s): 0 
Gene Names: nahF
Find proteins for Q1XGL7 (Pseudomonas putida)
Go to UniProtKB:  Q1XGL7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NK
Query on NK

Download SDF File 
Download CCD File 
A
SALICYLALDEHYDE
C7 H6 O2
SMQUZDBALVYZAC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.417 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 169.470α = 90.00
b = 169.470β = 90.00
c = 157.940γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHENIXrefinement
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references