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- PDB-9c0t: Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) hexa... -

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Basic information

Entry
Database: PDB / ID: 9c0t
TitleCarbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) hexamer from Methanosarcina thermophila
Components(Acetyl-CoA decarbonylase/synthase complex subunit ...) x 3
KeywordsOXIDOREDUCTASE / CO-dehydrogenase / acetyl-CoA synthase / Methanosarcina thermophila
Function / homology
Function and homology information


methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / acetyltransferase activity / nickel cation binding / iron-sulfur cluster binding ...methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / acetyltransferase activity / nickel cation binding / iron-sulfur cluster 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 beta, archaeal / 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 / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / Hydroxylamine reductase/Ni-containing CO dehydrogenase ...Acetyl-CoA decarbonylase/synthase complex subunit beta, archaeal / 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 / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / 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
CARBON MONOXIDE / NICKEL (II) ION / 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 / Acetyl-CoA decarbonylase/synthase complex subunit beta 2
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
Revision 1.1Oct 30, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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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
E: Acetyl-CoA decarbonylase/synthase complex subunit beta 2
F: Acetyl-CoA decarbonylase/synthase complex subunit beta 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,76723
Polymers318,4916
Non-polymers4,27617
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

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Acetyl-CoA decarbonylase/synthase complex subunit ... , 3 types, 6 molecules ABCDEF

#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: Protein Acetyl-CoA decarbonylase/synthase complex subunit beta 2 / ACDS complex subunit beta 2 / ACDS complex acyltransferase 2


Mass: 52802.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina thermophila (archaea)
References: UniProt: Q9V2Z4, CO-methylating acetyl-CoA synthase

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Non-polymers , 4 types, 17 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO

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Details

Has ligand of interestY
Has protein modificationY

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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, with two acetyl-CoA synthase beta subunits
Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 0.318 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
VitrificationCryogen name: ETHANE / Humidity: 82 % / Chamber temperature: 298 K / Details: SPT Labtech chameleon plunger

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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: 130000 X / Nominal defocus max: 1750 nm / Nominal defocus min: 0 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 47.1 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
11cryoSPARC3.3.2initial Euler assignment
12RELION4final Euler assignment
14RELION43D reconstruction
15PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1124872
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17073 / Symmetry type: POINT
Atomic model buildingB value: 67.9504 / 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_d0.00321071
ELECTRON MICROSCOPYf_angle_d0.53328577
ELECTRON MICROSCOPYf_dihedral_angle_d19.8022946
ELECTRON MICROSCOPYf_chiral_restr0.0433131
ELECTRON MICROSCOPYf_plane_restr0.0043684

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