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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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALDEHYDE OXIDOREDUCTASE
A
907Desulfovibrio gigasMutation(s): 0 
Gene Names: mop
EC: 1.2.99.7
Find proteins for Q46509 (Desulfovibrio gigas)
Go to UniProtKB:  Q46509
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BCT
Query on BCT

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A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FES
Query on FES

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A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

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A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
HCI
Query on HCI

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A
HYDROCINNAMIC ACID
3PP; 3-PHENYLPROPIONIC ACID
C9 H10 O2
XMIIGOLPHOKFCH-UHFFFAOYSA-N
 Ligand Interaction
PCD
Query on PCD

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A
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
MOLYBDENUM COFACTOR; MOCO
C19 H26 Mo N8 O16 P2 S2
YEBYDVFRFUQMER-NBXMTLLYDD
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-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 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 143.143α = 90.00
b = 143.143β = 90.00
c = 161.954γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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