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

Experimental Data Snapshot

  • Resolution: 2.42 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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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: https://doi.org/10.1021/acs.biochem.6b00614
  • Primary Citation of Related Structures:  

  • 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 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.

  • Organizational Affiliation

    Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte, MG 31270-901, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Salicylaldehyde dehydrogenase NahF500Pseudomonas putidaMutation(s): 0 
Gene Names: nahF
Find proteins for Q1XGL7 (Pseudomonas putida)
Explore Q1XGL7 
Go to UniProtKB:  Q1XGL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1XGL7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NK

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C7 H6 O2
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.47α = 90
b = 169.47β = 90
c = 157.94γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description