Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.97 kDa 
• Atom Count: 5559 
• Modelled Residue Count: 633 
• Deposited Residue Count: 636 
• Unique protein chains: 1

4UDX

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

• DOI: 10.2210/pdb4UDX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Carboxydothermus hydrogenoformans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-12 Released: 2015-05-13 
• Deposition Author(s): Fesseler, J., Jeoung, J.-H., Dobbek, H.

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Experimental Data Snapshot

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

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

• PubMed: 25926100 
• 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. 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(-).

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBON MONOXIDE DEHYDROGENASE 2	A [auth X]	636	Carboxydothermus hydrogenoformans	Mutation(s): 0  EC: 1.2.99.2 (PDB Primary Data), 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WCC	D [auth X]	FE(3)-NI(1)-S(4) CLUSTER Fe3 Ni S4 SEEZYPKDPRYISB-KUBGLCDSAO
SF4	B [auth X]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
FES	C [auth X]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE2	E [auth X]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CO2	F [auth X]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N

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 = 112.516	α = 90
b = 74.87	β = 111.26
c = 71.075	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-12 
• Released Date: 2015-05-13 
Deposition Author(s): Fesseler, J., Jeoung, J.-H., Dobbek, H.

Revision History  

• 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