8ON1

NI,FE-CODH -600mV state : 4 h Dioxygen Exposure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Stepwise O 2 -Induced Rearrangement and Disassembly of the [NiFe 4 (OH)( mu 3 -S) 4 ] Active Site Cluster of CO Dehydrogenase.

Basak, Y.Jeoung, J.H.Domnik, L.Dobbek, H.

(2023) Angew Chem Int Ed Engl 62: e202305341-e202305341

  • DOI: https://doi.org/10.1002/anie.202305341
  • Primary Citation of Related Structures:  
    8OMX, 8OMY, 8ON0, 8ON1, 8ON2, 8ON3

  • PubMed Abstract: 

    Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of carbon dioxide to carbon monoxide. CODHs are found in anaerobic microorganisms and can rapidly lose their activity when exposed to air. What causes the loss of activity is unclear. In this study, we analyzed the time-dependent structural changes induced by the presence of air on the metal centers of CODH-II. We show that inactivation is a multistep process. In a reversible step, the open coordination site on the Ni ion is blocked by a Ni,Fe-bridging μ-sulfido or chlorido ligand. Blocking this open coordination site with a cyanide ligand stabilizes the cluster against O 2 -induced decomposition, indicating that O 2 attacks at the Ni ion. In the subsequent irreversible phase, nickel is lost, the Fe ions rearrange and the sulfido ligands disappear. Our data are consistent with a reversible reductive reactivation mechanism to protect CODHs from transient over-oxidation.


  • Organizational Affiliation

    Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase 2A [auth X]636Carboxydothermus hydrogenoformans Z-2901Mutation(s): 0 
Gene Names: cooS2cooSIICHY_0085
EC: 1.2.7.4
UniProt
Find proteins for Q9F8A8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901))
Explore Q9F8A8 
Go to UniProtKB:  Q9F8A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F8A8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth X]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
C [auth X]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
J [auth X]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
D [auth X]
E [auth X]
F [auth X]
G [auth X]
H [auth X]
D [auth X],
E [auth X],
F [auth X],
G [auth X],
H [auth X],
I [auth X]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A [auth X]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.41α = 90
b = 75.36β = 111.44
c = 71.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyDO 785/6-2

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary