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- PDB-8uds: The Crystal Structure of CoxG from M. smegmatis, minus lipid anch... -

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Basic information

Entry
Database: PDB / ID: 8uds
TitleThe Crystal Structure of CoxG from M. smegmatis, minus lipid anchoring C-terminus.
ComponentsCarbon monoxide dehydrogenase subunit G (CoxG) family protein
KeywordsELECTRON TRANSPORT / Menaquinone Binding / Lipid Anchored / Carbon monoxide dehydrogenase / SRPBCC family protein
Function / homologyCarbon monoxide dehydrogenase subunit G / Carbon monoxide dehydrogenase subunit G (CoxG) / START-like domain superfamily / membrane / Carbon monoxide dehydrogenase subunit G (CoxG) family protein
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKropp, A. / Greening, C. / Grinter, R.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200103074 Australia
CitationJournal: Nat Chem Biol / Year: 2025
Title: Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria.
Authors: Ashleigh Kropp / David L Gillett / Hari Venugopal / Miguel A Gonzálvez / James P Lingford / Surbhi Jain / Christopher K Barlow / Jie Zhang / Chris Greening / Rhys Grinter /
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 ...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 (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.
History
DepositionSep 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Carbon monoxide dehydrogenase subunit G (CoxG) family protein


Theoretical massNumber of molelcules
Total (without water)18,0361
Polymers18,0361
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.095, 64.095, 87.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-317-

HOH

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Components

#1: Protein Carbon monoxide dehydrogenase subunit G (CoxG) family protein


Mass: 18036.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_0749 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3 / References: UniProt: A0QQG7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 % / Description: Diamonds
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.9 / Details: 0.1 M KSCN (Salt) 30 %w/v PEG MME 2K (Precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 14, 2022 / Details: Yes
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→45.32 Å / Num. obs: 29933 / % possible obs: 99.98 % / Observed criterion σ(I): 1.3 / Redundancy: 38.6 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.013 / Net I/σ(I): 33.4
Reflection shellResolution: 1.5→1.52 Å / Rmerge(I) obs: 4.24 / Num. unique obs: 1439 / CC1/2: 0.624 / Rpim(I) all: 0.0747

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.25 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1473 4.92 %
Rwork0.181 --
obs0.1834 29933 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 0 175 1272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061166
X-RAY DIFFRACTIONf_angle_d0.8671588
X-RAY DIFFRACTIONf_dihedral_angle_d4.998163
X-RAY DIFFRACTIONf_chiral_restr0.076189
X-RAY DIFFRACTIONf_plane_restr0.007210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.31581350.26432514X-RAY DIFFRACTION99
1.55-1.60.26421320.22032552X-RAY DIFFRACTION100
1.6-1.670.2761320.21762533X-RAY DIFFRACTION100
1.67-1.740.24931160.19512564X-RAY DIFFRACTION100
1.74-1.840.23261250.16092566X-RAY DIFFRACTION100
1.84-1.950.19611210.14972561X-RAY DIFFRACTION100
1.95-2.10.21081470.16652567X-RAY DIFFRACTION100
2.1-2.310.18741180.16552596X-RAY DIFFRACTION100
2.31-2.650.24271590.18612577X-RAY DIFFRACTION100
2.65-3.330.24331260.19452656X-RAY DIFFRACTION100
3.33-40.250.22231620.17632774X-RAY DIFFRACTION100

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