4UDX

CO2 bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.157 
  • R-Value Observed: 0.132 

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This is version 2.1 of the entry. See complete history. 


Literature

How the [NiFe4S4] Cluster of CO Dehydrogenase Activates CO2 and NCO(-).

Fesseler, J., Jeoung, J.H., Dobbek, H.

(2015) Angew Chem Int Ed Engl 54: 8560-8564

  • DOI: 10.1002/anie.201501778
  • Primary Citation of Related Structures:  
    4UDX, 4UDY

  • PubMed Abstract: 

    • Ni,Fe-containing CO dehydrogenases (CODHs) use a [NiFe4S4] cluster, termed cluster C, to reversibly reduce CO2 to CO with high turnover number. Binding to Ni and Fe activates CO2, but current crystal structures have insufficient resolution to analyze the geometry of bound CO2 and reveal the extent and nature of its activation ...

    Ni,Fe-containing CO dehydrogenases (CODHs) use a [NiFe4S4] cluster, termed cluster C, to reversibly reduce CO2 to CO with high turnover number. Binding to Ni and Fe activates CO2, but current crystal structures have insufficient resolution to analyze the geometry of bound CO2 and reveal the extent and nature of its activation. The crystal structures of CODH in complex with CO2 and the isoelectronic inhibitor NCO(-) are reported at true atomic resolution (dmin ≤1.1 Å). Like CO2, NCO(-) is a μ2,η(2) ligand of the cluster and acts as a mechanism-based inhibitor. While bound CO2 has the geometry of a carboxylate group, NCO(-) is transformed into a carbamoyl group, thus indicating that both molecules undergo a formal two-electron reduction after binding and are stabilized by substantial π backbonding. The structures reveal the combination of stable μ2,η(2) coordination by Ni and Fe2 with reductive activation as the basis for both the turnover of CO2 and inhibition by NCO(-).

    Organizational Affiliation: 

    Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin (Germany). holger.dobbek@hu-berlin.de.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBON MONOXIDE DEHYDROGENASE 2A [auth X]636Carboxydothermus hydrogenoformansMutation(s): 0 
EC: 1.2.99.2 (PDB Primary Data), 1.2.7.4 (UniProt)
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WCC
Query on WCC
Download Ideal Coordinates CCD File 
D [auth X]FE(3)-NI(1)-S(4) CLUSTER
Fe3 Ni S4
SEEZYPKDPRYISB-KUBGLCDSAO		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
B [auth X]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
C [auth X]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
E [auth X]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
CO2
Query on CO2
Download Ideal Coordinates CCD File 
F [auth X]CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.157 
  • R-Value Observed: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.516α = 90
b = 74.87β = 111.26
c = 71.075γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
XSCALEdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Refinement description
  • Version 2.0: 2019-01-23
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2019-05-22
    Changes: Data collection, Refinement description