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- PDB-9c0q: Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermoph... -

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Basic information

Entry
Database: PDB / ID: 9c0q
TitleCarbon monoxide dehydrogenase (CODH) from Methanosarcina thermophila, specimen prepared on blot plunger
Components
  • Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
  • Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
KeywordsOXIDOREDUCTASE / CO-dehydrogenase
Function / homology
Function and homology information


methanogenesis, from acetate / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / acetyl-CoA metabolic process / nickel cation binding / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / DHS-like NAD/FAD-binding domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site ...Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / DHS-like NAD/FAD-binding domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Fe(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2 / Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBiester, A. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy.
Authors: Alison Biester / David A Grahame / Catherine L Drennan /
Abstract: Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A- ...Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from (CODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our CODH/ACS structure with our CODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization.
History
DepositionMay 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
B: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
C: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
D: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,16913
Polymers212,8864
Non-polymers3,2829
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Acetyl-CoA decarbonylase/synthase complex subunit alpha 2 / ACDS complex subunit alpha 2 / ACDS complex carbon monoxide dehydrogenase subunit alpha 2 / ACDS ...ACDS complex subunit alpha 2 / ACDS complex carbon monoxide dehydrogenase subunit alpha 2 / ACDS CODH subunit alpha 2


Mass: 87855.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina thermophila (archaea)
References: UniProt: Q9C4Z4, anaerobic carbon monoxide dehydrogenase
#2: Protein Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2 / ACDS complex subunit epsilon 2 / ACDS complex carbon monoxide dehydrogenase subunit epsilon 2 / ...ACDS complex subunit epsilon 2 / ACDS complex carbon monoxide dehydrogenase subunit epsilon 2 / ACDS CODH subunit epsilon 2


Mass: 18587.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina thermophila (archaea) / References: UniProt: Q9C4Z3
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-RQM / Fe(3)-Ni(1)-S(4) cluster


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Acetyl-CoA decarbonylase/synthase complex / Type: COMPLEX
Details: Carbon monoxide dehydrogenase heterotetramer, alpha and epsilon subunits
Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.212 MDa / Experimental value: NO
Source (natural)Organism: Methanosarcina thermophila (archaea)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMMOPSC7H15NO4S1
225 mMSodium sulfateNa2SO41
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 54.53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
2EPUimage acquisition
7UCSF ChimeraX1.6.1model fitting
8PHENIX1.21.1_5286model fitting
9Coot0.9.8.92model fitting
11PHENIX1.21.1_5286model refinement
12cryoSPARC3.3.2initial Euler assignment
13RELION4final Euler assignment
14RELION4classification
15RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 852015
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99894 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 90.5204 / Space: REAL / Target criteria: Correlation coefficient
Details: Initial model was generated using AlphaFold, fit to the map using ChimeraX, followed by rigid body fitting in phenix, and finally iterative real space refinement in coot and phenix.
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314566
ELECTRON MICROSCOPYf_angle_d0.55619790
ELECTRON MICROSCOPYf_dihedral_angle_d20.7272072
ELECTRON MICROSCOPYf_chiral_restr0.0422210
ELECTRON MICROSCOPYf_plane_restr0.0042540

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