3NW4

Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with gentisate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The salicylate 1,2-dioxygenase as a model for a conventional gentisate 1,2-dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate.

Ferraroni, M.Matera, I.Burger, S.Reichert, S.Steimer, L.Scozzafava, A.Stolz, A.Briganti, F.

(2013) FEBS J. 280: 1643-1652

  • DOI: 10.1111/febs.12173
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The salicylate 1,2-dioxygenase (SDO) from the bacterium Pseudaminobacter salicylatoxidans BN12 is a versatile gentisate 1,2-dioxygenase (GDO) that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates. Several varian ...

    The salicylate 1,2-dioxygenase (SDO) from the bacterium Pseudaminobacter salicylatoxidans BN12 is a versatile gentisate 1,2-dioxygenase (GDO) that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates. Several variants of this enzyme were rationally designed based on the previously determined enzyme structure and sequence differences between the SDO and the 'conventional' GDO from Corynebacterium glutamicum. This was undertaken in order to define the structural elements that give the SDO its unique ability to dioxygenolytically cleave (substituted) salicylates. SDO variants M103L, G106A, G111A, R113G, S147R and F159Y were constructed and it was found that G106A oxidized only gentisate; 1-hydroxy-2-naphthoate and salicylate were not converted. This indicated that this enzyme variant behaves like previously known 'conventional' GDOs. Crystals of the G106A SDO variant and its complexes with salicylate and gentisate were obtained under anaerobic conditions, and the structures were solved and analyzed. The amino acid residue Gly106 is located inside the SDO active site cavity but does not directly interact with the substrates. Crystal structures of G106A SDO complexes with gentisate and salicylate showed a different binding mode for salicylate when compared with the wild-type enzyme. Thus, salicylate coordinated in the G106A variant with the catalytically active Fe(II) ion in an unusual and unproductive manner because of the inability of salicylate to displace a hydrogen bond that was formed between Trp104 and Asp174 in the G106A variant. It is proposed that this type of unproductive substrate binding might generally limit the substrate spectrum of 'conventional' GDOs.


    Organizational Affiliation

    Dipartimento di Chimica Ugo Schiff, Università di Firenze, Sesto Fiorentino, Italy. marta.ferraroni@unifi.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gentisate 1,2-Dioxygenase
A
368Pseudaminobacter salicylatoxidansMutation(s): 1 
Find proteins for Q67FT0 (Pseudaminobacter salicylatoxidans)
Go to UniProtKB:  Q67FT0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
GTQ
Query on GTQ

Download SDF File 
Download CCD File 
A
2,5-dihydroxybenzoic acid
C7 H6 O4
WXTMDXOMEHJXQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.158 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.500α = 90.00
b = 86.890β = 90.00
c = 166.830γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DNAdata collection
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release