4US9 | pdb_00004us9

Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with 3- phenylpropionaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.117 (Depositor), 0.130 (DCC) 
  • R-Value Work: 
    0.093 (Depositor), 0.112 (DCC) 
  • R-Value Observed: 
    0.095 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1007/s00775-014-1196-4
  • Primary Citation Related Structures: 
    4US8, 4US9, 4USA

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 98.78 kDa 
  • Atom Count: 8,621 
  • Modeled Residue Count: 907 
  • Deposited Residue Count: 907 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALDEHYDE OXIDOREDUCTASE907Megalodesulfovibrio gigasMutation(s): 0 
EC: 1.2.99.7
UniProt
Find proteins for Q46509 (Megalodesulfovibrio gigas)
Explore Q46509 
Go to UniProtKB:  Q46509
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46509
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCD

Query on PCD



Download:Ideal Coordinates CCD File
M [auth A](MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
C19 H26 Mo N8 O16 P2 S2
YEBYDVFRFUQMER-MQPNXHJTSA-L
FES

Query on FES



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
3PL

Query on 3PL



Download:Ideal Coordinates CCD File
D [auth A]3-PHENYLPROPANAL
C9 H10 O
YGCZTXZTJXYWCO-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.117 (Depositor), 0.130 (DCC) 
  • R-Value Work:  0.093 (Depositor), 0.112 (DCC) 
  • R-Value Observed: 0.095 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.766α = 90
b = 143.766β = 90
c = 162.544γ = 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: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary