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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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.,Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin (Germany).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBON MONOXIDE DEHYDROGENASE 2
X
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 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
WCC
Query on WCC

Download SDF File 
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
CO2
Query on CO2

Download SDF File 
Download CCD File 
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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.516α = 90.00
b = 74.870β = 111.26
c = 71.075γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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