6ELQ

Carbon Monoxide Dehydrogenase IV from Carboxydothermus hydrogenoformans

• PDB DOI:  https://doi.org/10.2210/pdb6ELQ/pdb

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


• Deposited: 2017-09-29 Released: 2018-01-03 
• Deposition Author(s): Domnik, L., Goetzl, S., Jeoung, J.H., Dobbek, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.275 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 

Literature

CODH-IV: A High-Efficiency CO-Scavenging CO Dehydrogenase with Resistance to O2.

Domnik, L., Merrouch, M., Goetzl, S., Jeoung, J.H., Leger, C., Dementin, S., Fourmond, V., Dobbek, H.

(2017) Angew Chem Int Ed Engl 56: 15466-15469

• PubMed: 29024326 
• DOI: https://doi.org/10.1002/anie.201709261
• Primary Citation of Related Structures:  
  6ELQ


• PubMed Abstract: 
  

CO dehydrogenases (CODHs) catalyse the reversible conversion between CO and CO ₂ . Genomic analysis indicated that the metabolic functions of CODHs vary. The genome of Carboxydothermus hydrogenoformans encodes five CODHs (CODH-I-V), of which CODH-IV is found in a gene cluster near a peroxide-reducing enzyme. Our kinetic and crystallographic experiments reveal that CODH-IV differs from other CODHs in several characteristic properties: it has a very high affinity for CO, oxidizes CO at diffusion-limited rate over a wide range of temperatures, and is more tolerant to oxygen than CODH-II. Thus, our observations support the idea that CODH-IV is a CO scavenger in defence against oxidative stress and highlight that CODHs are more diverse in terms of reactivity than expected.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 208.05 kDa 
• Atom Count: 14,594 
• Modelled Residue Count: 1,890 
• Deposited Residue Count: 1,899 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon Monoxide Dehydrogenase	A [auth X], B [auth A], C [auth B]	633	Carboxydothermus hydrogenoformans	Mutation(s): 0  Gene Names: cooSIV EC: 1.2.7.4
UniProt
Find proteins for Q3AE44 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3AE44  Go to UniProtKB:  Q3AE44

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BF8	E [auth X], H [auth A], K [auth B]	FE(4)-NI(1)-S(5) CLUSTER with Oxygen Fe4 Ni O S4 DGNZLMZPCMYVGP-UHFFFAOYSA-N
SF4	D [auth X], F [auth A], G [auth A], I [auth B], J [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.275 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.15	α = 90
b = 209.15	β = 90
c = 93.41	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-03 
Deposition Author(s): Domnik, L., Goetzl, S., Jeoung, J.H., Dobbek, H.

Revision History  

• Version 1.0: 2018-01-03
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection