4USA

Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with trans-cinnamaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.102 
  • R-Value Observed: 0.103 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Aromatic Aldehydes at the Active Site of Aldehyde Oxidoreductase from Desulfovibrio Gigas: Reactivity and Molecular Details of the Enzyme-Substrate and Enzyme-Product Interaction.

Correia, H.D.Marangon, J.Brondino, C.D.Moura, J.J.G.Romao, M.J.Gonzalez, P.J.Santos-Silva, T.

(2015) J Biol Inorg Chem 20: 219

  • DOI: 10.1007/s00775-014-1196-4
  • Primary Citation of Related Structures:  
    4USA, 4US8, 4US9

  • PubMed Abstract: 
  • Desulfovibrio gigas aldehyde oxidoreductase (DgAOR) is a mononuclear molybdenum-containing enzyme from the xanthine oxidase (XO) family, a group of enzymes capable of catalyzing the oxidative hydroxylation of aldehydes and heterocyclic compounds. The kinetic studies reported in this work showed that DgAOR catalyzes the oxidative hydroxylation of aromatic aldehydes, but not heterocyclic compounds ...

    Desulfovibrio gigas aldehyde oxidoreductase (DgAOR) is a mononuclear molybdenum-containing enzyme from the xanthine oxidase (XO) family, a group of enzymes capable of catalyzing the oxidative hydroxylation of aldehydes and heterocyclic compounds. The kinetic studies reported in this work showed that DgAOR catalyzes the oxidative hydroxylation of aromatic aldehydes, but not heterocyclic compounds. NMR spectroscopy studies using (13)C-labeled benzaldehyde confirmed that DgAOR catalyzes the conversion of aldehydes to the respective carboxylic acids. Steady-state kinetics in solution showed that high concentrations of the aromatic aldehydes produce substrate inhibition and in the case of 3-phenyl propionaldehyde a suicide substrate behavior. Hydroxyl-substituted aromatic aldehydes present none of these behaviors but the kinetic parameters are largely affected by the position of the OH group. High-resolution crystallographic structures obtained from single crystals of active-DgAOR soaked with benzaldehyde showed that the side chains of Phe425 and Tyr535 are important for the stabilization of the substrate in the active site. On the other hand, the X-ray data of DgAOR soaked with trans-cinnamaldehyde showed a cinnamic acid molecule in the substrate channel. The X-ray data of DgAOR soaked with 3-phenyl propionaldehyde showed clearly how high substrate concentrations inactivate the enzyme by binding covalently at the surface of the enzyme and blocking the substrate channel. The different reactivity of DgAOR versus aldehyde oxidase and XO towards aromatic aldehydes and N-heterocyclic compounds is explained on the basis of the present kinetic and structural data.


    Organizational Affiliation

    UCIBIO@REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALDEHYDE OXIDOREDUCTASEA907Desulfovibrio gigasMutation(s): 0 
Gene Names: mop
EC: 1.2.99.7
UniProt
Find proteins for Q46509 (Desulfovibrio gigas)
Explore Q46509 
Go to UniProtKB:  Q46509
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCD (Subject of Investigation/LOI)
Query on PCD

Download Ideal Coordinates CCD File 
L [auth A](MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
C19 H26 Mo N8 O16 P2 S2
YEBYDVFRFUQMER-NBXMTLLYDD
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HCI (Subject of Investigation/LOI)
Query on HCI

Download Ideal Coordinates CCD File 
M [auth A]HYDROCINNAMIC ACID
C9 H10 O2
XMIIGOLPHOKFCH-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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E [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
D [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A], K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.102 
  • R-Value Observed: 0.103 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.143α = 90
b = 143.143β = 90
c = 161.954γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Data collection
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation