8UDS | pdb_00008uds

The Crystal Structure of CoxG from M. smegmatis, minus lipid anchoring C-terminus.

• PDB DOI: https://doi.org/10.2210/pdb8UDS/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-29 Released: 2024-10-02 
• Deposition Author(s): Kropp, A., Greening, C., Grinter, R.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: in silico

Literature

Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria.

Kropp, A., Gillett, D.L., Venugopal, H., Gonzalvez, M.A., Lingford, J.P., Jain, S., Barlow, C.K., Zhang, J., Greening, C., Grinter, R.

(2025) Nat Chem Biol 21: 1058-1068

• PubMed: 39881213 
• DOI: https://doi.org/10.1038/s41589-025-01836-0
• Primary Citation of Related Structures:  
  8UDS, 8UEM


• PubMed Abstract: 
  

  Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring the obtained electrons to the aerobic respiratory chain. However, it is unknown how these enzymes oxidize CO at low concentrations and interact with the respiratory chain. Here, we use cryo-electron microscopy and structural modeling to show how Mo-CODH _Ms (CoxSML) from Mycobacterium smegmatis interacts with its partner, the membrane-bound menaquinone-binding protein CoxG. We provide electrochemical, biochemical and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chain through CoxG. Lastly, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of the biogeochemically and ecologically important process of atmospheric CO oxidation, while demonstrating that long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.

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Organizational Affiliation: 
• Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Ramaciotti Centre for Cryo-Electron Microscopy, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
School of Chemistry, Monash University, Clayton, Victoria, Australia.
Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Monash Proteomics & Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
ARC Centre of Excellence for Green Electrochemical Transformation of Carbon Dioxide, Monash University, Clayton, Victoria, Australia.
ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, USA.
Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, USA. [e-mail].
Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, USA. [e-mail].
Centre to Impact AMR, Monash University, Clayton, Victoria, USA. [e-mail].
Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia. [e-mail].
Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.04 kDa 
• Atom Count: 1,312 
• Modeled Residue Count: 147 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase subunit G (CoxG) family protein	A [auth D]	167	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_0749
UniProt
Find proteins for A0QQG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQG7  Go to UniProtKB:  A0QQG7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.095	α = 90
b = 64.095	β = 90
c = 87.539	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Kropp, A., Greening, C., Grinter, R.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP200103074

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references, Structure summary
• Version 1.2: 2025-02-12
  Changes: Database references
• Version 1.3: 2025-07-09
  Changes: Database references