8UEM

The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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 

  • 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.


  • Organizational Affiliation

    Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase (Large chain), CoxL
A, D
799Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for O53708 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53708 
Go to UniProtKB:  O53708
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53708
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase medium chain
B, E
296Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for I6Y7N2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6Y7N2 
Go to UniProtKB:  I6Y7N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6Y7N2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
[2Fe-2S] binding domain protein
C, F
158Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for O53709 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53709 
Go to UniProtKB:  O53709
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53709
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
I [auth B],
N [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MCN (Subject of Investigation/LOI)
Query on MCN

Download Ideal Coordinates CCD File 
H [auth A],
M [auth D]
PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
CUN (Subject of Investigation/LOI)
Query on CUN

Download Ideal Coordinates CCD File 
G [auth A],
L [auth D]
CU(I)-S-MO(IV)(=O)OH CLUSTER
Cu H Mo O2 S
GIYZUGIRDQLYSY-UHFFFAOYSA-M
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
J [auth C],
K [auth C],
O [auth F],
P [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1.2
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP200103074

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-02-12
    Changes: Data collection, Database references