3L4P

Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase.

Thapper, A.Boer, D.R.Brondino, C.D.Moura, J.J.Romao, M.J.

(2007) J Biol Inorg Chem 12: 353-366

  • DOI: 10.1007/s00775-006-0191-9
  • Primary Citation of Related Structures:  
    3L4P

  • PubMed Abstract: 
  • Two arsenite-inhibited forms of each of the aldehyde oxidoreductases from Desulfovibrio gigas and Desulfovibrio desulfuricans have been studied by X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy. The molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis ...

    Two arsenite-inhibited forms of each of the aldehyde oxidoreductases from Desulfovibrio gigas and Desulfovibrio desulfuricans have been studied by X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy. The molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. Arsenite addition to active as-prepared enzyme or to a reduced desulfo form yields two different species called A and B, respectively, which show different Mo(V) EPR signals. Both EPR signals show strong hyperfine and quadrupolar couplings with an arsenic nucleus, which suggests that arsenic interacts with molybdenum through an equatorial ligand. X-ray data of single crystals prepared from EPR-active samples show in both inhibited forms that the arsenic atom interacts with the molybdenum ion through an oxygen atom at the catalytic labile site and that the sulfido ligand is no longer present. EPR and X-ray data indicate that the main difference between both species is an equatorial ligand to molybdenum which was determined to be an oxo ligand in species A and a hydroxyl/water ligand in species B. The conclusion that the sulfido ligand is not essential to determine the EPR properties in both Mo-As complexes is achieved through EPR measurements on a substantial number of randomly oriented chemically reduced crystals immediately followed by X-ray studies on one of those crystals. EPR saturation studies show that the electron transfer pathway, which is essential for catalysis, is not modified upon inhibition.


    Organizational Affiliation

    REQUIMTE-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D 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
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCD (Subject of Investigation/LOI)
Query on PCD

Download Ideal Coordinates CCD File 
T [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

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B [auth A], C [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
AST
Query on AST

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U [auth A]ARSENITE
As O3
OWTFKEBRIAXSMO-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

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V [auth A], W [auth A], X [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
URE
Query on URE

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R [auth A]UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Y [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , O [auth A] , P [auth A] , Q [auth A] , 
J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

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I [auth A]LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.89α = 90
b = 142.89β = 90
c = 161.64γ = 120
Software Package:
Software NamePurpose
ProDCdata collection
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-12-21 
  • Released Date: 2010-02-16 
  • Deposition Author(s): Boer, D.R., Romao, M.J.
  • This entry supersedes: 1ZCS

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-11-13
    Changes: Advisory, Data collection