3I39

NI,FE-CODH-320 MV+CN state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of cyanide inhibition of Ni, Fe-containing carbon monoxide dehydrogenase

Jeoung, J.H.Dobbek, H.

(2009) J.Am.Chem.Soc. 131: 9922-9923

  • DOI: 10.1021/ja9046476

  • PubMed Abstract: 
  • Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of carbon monoxide with water to carbon dioxide, two protons, and two electrons. The CODHs of anaerobic microorganisms harbor a complex Ni/Fe/S-containing metal center called a ...

    Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of carbon monoxide with water to carbon dioxide, two protons, and two electrons. The CODHs of anaerobic microorganisms harbor a complex Ni/Fe/S-containing metal center called a C-cluster in their active site, which activates the substrates water and carbon monoxide, stabilizes an intermediary metal-carboxylate, and transiently stores the two electrons generated in the reaction. Several small molecules have been reported to inhibit carbon monoxide oxidation by CODHs, among which the cyanide anion acts as a slow binding inhibitor. Cyanide is isoelectronic to the substrate carbon monoxide, and its binding to the C-cluster has been reported to involve nickel, nickel and iron, or only iron. We report the crystal structure of CODH-II from Carboxydothermus hydrogenoformans in complex with cyanide at 1.36 A resolution. The structure reveals that cyanide binds to the C-cluster at an open coordination site completing the square-planar coordination geometry of the nickel ion. While active CODH has a water/hydroxo-ligand bound to an iron ion near nickel, in the cyanide complex the water/hydroxo-ligand is lost and iron occupies a position more close to the nickel ion. Based on the structure, we suggest that the competitive inhibitory character of cyanide originates from it obstruction of carbon monoxide binding to the nickel ion while the slow binding inhibition is due to a conformational change of the protein during which the water/hydroxo-ligand bound to iron is lost.


    Organizational Affiliation

    Labor für Bioanorganische Chemie, Universität Bayreuth, 95447 Bayreuth, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase 2
X
656Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)Mutation(s): 1 
Gene Names: cooS2 (cooSII)
EC: 1.2.7.4
Find proteins for Q9F8A8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901))
Go to UniProtKB:  Q9F8A8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
X
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CYN
Query on CYN

Download SDF File 
Download CCD File 
X
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
WCC
Query on WCC

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Download CCD File 
X
FE(3)-NI(1)-S(4) CLUSTER
C CLUSTER CUBANE
Fe3 Ni S4
SEEZYPKDPRYISB-KUBGLCDSAO
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
X
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
X
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.279α = 90.00
b = 75.834β = 111.33
c = 71.099γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
MAR345dtbdata collection
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance