1SU7

Carbon Monoxide Dehydrogenase from Carboxydothermus hydrogenoformans- DTT reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase

Dobbek, H.Svetlitchnyi, V.Liss, J.Meyer, O.

(2004) J.Am.Chem.Soc. 126: 5382-5387

  • DOI: 10.1021/ja037776v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During the past two years, crystal structures of Cu- and Mo-containing carbon monoxide dehydrogenases (CODHs) and Ni- and Fe-containing CODHs have been reported. The active site of CODHs from anaerobic bacteria (cluster C) is composed of Ni, Fe, and ...

    During the past two years, crystal structures of Cu- and Mo-containing carbon monoxide dehydrogenases (CODHs) and Ni- and Fe-containing CODHs have been reported. The active site of CODHs from anaerobic bacteria (cluster C) is composed of Ni, Fe, and S for which crystallographic studies of the enzymes from Carboxydothermus hydrogenoformans, Rhodospirillum rubrum, and Moorella thermoaceticarevealed structural similarities in the overall protein fold but showed substantial differences in the essential Ni coordination environment. The [Ni-4Fe-5S] cluster C in the fully catalytically competent dithionite-reduced CODH II from C. hydrogenoformans (CODHII(Ch)) at 1.6 A resolution contains a characteristic mu(2)-sulfido ligand between Ni and Fe1, resulting in a square-planar ligand arrangement with four S-ligands at the Ni ion. In contrast, the [Ni-4Fe-4S] clusters C in CO-treated CODH from R. rubrum resolved at 2.8 A and in CO-treated acetyl-CoA synthase/CODH complex from M. thermoacetica at 2.2 and 1.9 A resolution, respectively, do not contain the mu(2)-sulfido ligand between Ni and Fe1 and display dissimilar geometries at the Ni ion. The [Ni-4Fe-4S] cluster is composed of a cubane [Ni-3Fe-4S] cluster linked to a mononuclear Fe site. The described coordination geometries of the Ni ion in the [Ni-4Fe-4S] cluster of R. rubrum and M. thermoacetica deviate from the square-planar ligand geometry in the [Ni-4Fe-5S] cluster C of CODHII(Ch). In addition, the latter was converted into a [Ni-4Fe-4S] cluster under specific conditions. The objective of this study was to elucidate the relationship between the structure of cluster C in CODHII(Ch) and the functionality of the protein. We have determined the CO oxidation activity of CODHII(Ch) under different conditions of crystallization, prepared crystals of the enzyme in the presence of dithiothreitol or dithionite as reducing agents under an atmosphere of N(2) or CO, and solved the corresponding structures at 1.1 to 1.6 A resolutions. Fully active CODHII(Ch) obtained after incubation of the enzyme with dithionite under N(2) revealed the [Ni-4Fe-5S] cluster. Short treatment of the enzyme with CO in the presence of dithiothreitol resulted in a catalytically competent CODHII(Ch) with a CO-reduced [Ni-4Fe-5S] cluster, but a prolonged treatment with CO caused the loss of CO-oxidizing activity and revealed a [Ni-4Fe-4S] cluster, which did not contain a mu(2)-S. These data suggest that the [Ni-4Fe-4S] cluster of CODHII(Ch) is an inactivated decomposition product originating from the [Ni-4Fe-5S] cluster.


    Organizational Affiliation

    Laboratorium für Proteinkristallographie, Universität Bayreuth, Bayreuth, Germany. Holger.Dobbeck@uni-bayreuth.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase 2
A
636Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)Mutation(s): 0 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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

Download SDF File 
Download CCD File 
A
FE(4)-NI(1)-S(5) CLUSTER
Fe4 Ni S5
DHBVHUGSWMHFLY-KYYUWLETAR
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.138 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.616α = 90.00
b = 73.825β = 111.17
c = 70.832γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SHELXL-97refinement
XDSdata reduction
CNSrefinement
XDSdata scaling
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description