4CFS

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Origin of the Proton-Transfer Step in the Cofactor-Free 1-H-3-Hydroxy-4-Oxoquinaldine 2,4- Dioxygenase: Effect of the Basicity of an Active Site His Residue.

Hernandez-Ortega, A.Quesne, M.G.Bui, S.Heuts, D.P.Steiner, R.A.Heyes, D.J.De Visser, S.P.Scrutton, N.S.

(2014) J Biol Chem 289: 8620

  • DOI: 10.1074/jbc.M113.543033
  • Primary Citation of Related Structures:  
    4CFS

  • PubMed Abstract: 
  • Dioxygenases catalyze a diverse range of chemical reactions that involve the incorporation of oxygen into a substrate and typically use a transition metal or organic cofactor for reaction. Bacterial (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) belongs to a class of oxygenases able to catalyze this energetically unfavorable reaction without any cofactor ...

    Dioxygenases catalyze a diverse range of chemical reactions that involve the incorporation of oxygen into a substrate and typically use a transition metal or organic cofactor for reaction. Bacterial (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) belongs to a class of oxygenases able to catalyze this energetically unfavorable reaction without any cofactor. In the quinaldine metabolic pathway, HOD breaks down its natural N-heteroaromatic substrate using a mechanism that is still incompletely understood. Experimental and computational approaches were combined to study the initial step of the catalytic cycle. We have investigated the role of the active site His-251/Asp-126 dyad, proposed to be involved in substrate hydroxyl group deprotonation, a critical requirement for subsequent oxygen reaction. The pH profiles obtained under steady-state conditions for the H251A and D126A variants show a strong pH effect on their kcat and kcat/Km constants, with a decrease in kcat/Km of 5500- and 9-fold at pH 10.5, respectively. Substrate deprotonation studies under transient-state conditions show that this step is not rate-limiting and yield a pKa value of ∼ 7.2 for WT HOD. A large solvent isotope effect was found, and the pKa value was shifted to ∼ 8.3 in D2O. Crystallographic and computational studies reveal that the mutations have a minor effect on substrate positioning. Computational work shows that both His-251 and Asp-126 are essential for the proton transfer driving force of the initial reaction. This multidisciplinary study offers unambiguous support to the view that substrate deprotonation, driven by the His/Asp dyad, is an essential requirement for its activation.


    Related Citations: 
    • Structural Basis for Cofactor-Independent Dioxygenation of N-Heteroaromatic Compounds at the Alpha/Beta-Hydrolase Fold.
      Steiner, R.A., Janssen, H.J., Roversi, P., Oakley, A.J., Fetzner, S.
      (2010) Proc Natl Acad Sci U S A 107: 657

    Organizational Affiliation

    From the Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASEA, B, C, D287Paenarthrobacter nitroguajacolicusMutation(s): 2 
Gene Names: hodmeqEARUE_113p00080pAL1.008
EC: 1.13.11.48
UniProt
Find proteins for O31266 (Paenarthrobacter nitroguajacolicus)
Explore O31266 
Go to UniProtKB:  O31266
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31266
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HQD
Query on HQD

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
P [auth D]
3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE
C10 H9 N O2
FSCXZVPPDJYLDD-UHFFFAOYSA-N
 Ligand Interaction
TAR
Query on TAR

Download Ideal Coordinates CCD File 
G [auth A],
L [auth C],
M [auth C],
N [auth C],
Q [auth D],
G [auth A],
L [auth C],
M [auth C],
N [auth C],
Q [auth D],
R [auth D],
S [auth D]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
O [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.73α = 90
b = 166.85β = 90
c = 167.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2014-04-02
    Changes: Database references