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- EMDB-45091: Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pent... -

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Entry
Database: EMDB / ID: EMD-45091
TitleCarbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila
Map dataCarbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila
Sample
  • Complex: Acetyl-CoA decarbonylase/synthase complex
    • Protein or peptide: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
    • Protein or peptide: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
    • Protein or peptide: Acetyl-CoA decarbonylase/synthase complex subunit beta 2
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Fe(3)-Ni(1)-S(4) cluster
  • Ligand: FE3-S4 CLUSTER
  • Ligand: CARBON MONOXIDE
  • Ligand: NICKEL (II) ION
KeywordsCO-dehydrogenase / acetyl-CoA synthase / Methanosarcina thermophila / OXIDOREDUCTASE
Function / homology
Function and homology information


methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / acetyl-CoA metabolic process / acetyltransferase activity / iron-sulfur cluster binding / nickel cation binding ...methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / acetyl-CoA metabolic process / acetyltransferase activity / iron-sulfur cluster binding / 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 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBiester A / Drennan CL
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45091.png

Downloads & links

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Map

FileDownload / File: emd_45091.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCarbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 261.6 Å		0.65 Å/pix.
x 400 pix.
= 261.6 Å		0.65 Å/pix.
x 400 pix.
= 261.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.019059317 - 0.040615045
Average (Standard dev.)0.0000372494 (±0.00085003005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 261.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45091_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half Map B

Fileemd_45091_half_map_1.map
AnnotationHalf Map B
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_45091_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : Acetyl-CoA decarbonylase/synthase complex

EntireName: Acetyl-CoA decarbonylase/synthase complex
Components
  • Complex: Acetyl-CoA decarbonylase/synthase complex
    • Protein or peptide: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
    • Protein or peptide: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
    • Protein or peptide: Acetyl-CoA decarbonylase/synthase complex subunit beta 2
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Fe(3)-Ni(1)-S(4) cluster
  • Ligand: FE3-S4 CLUSTER
  • Ligand: CARBON MONOXIDE
  • Ligand: NICKEL (II) ION

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Supramolecule #1: Acetyl-CoA decarbonylase/synthase complex

SupramoleculeName: Acetyl-CoA decarbonylase/synthase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Carbon monoxide dehydrogenase heterotetramer, alpha and epsilon subunits, with acetyl-CoA synthase beta subunit
Source (natural)Organism: Methanosarcina thermophila (archaea)
Molecular weightTheoretical: 265 KDa

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Macromolecule #1: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2

MacromoleculeName: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: anaerobic carbon monoxide dehydrogenase
Source (natural)Organism: Methanosarcina thermophila (archaea)
Molecular weightTheoretical: 87.855852 KDa
SequenceString: MSKLTTGSFS IEDLESVQIT INNIVGAAKE AAEKAEEELG PMGPTPFPTA ATVRDWSFTL FDRYEPVYTP MCDQCCYCTF GPCNLEGNR RGACGLDMKG QAAREFFLRC ITGCACHSAH GRHLLDHIIS IFGEDMPINM GASNVIAPNI QLITGRQPKT L GDLKPIME ...String:
MSKLTTGSFS IEDLESVQIT INNIVGAAKE AAEKAEEELG PMGPTPFPTA ATVRDWSFTL FDRYEPVYTP MCDQCCYCTF GPCNLEGNR RGACGLDMKG QAAREFFLRC ITGCACHSAH GRHLLDHIIS IFGEDMPINM GASNVIAPNI QLITGRQPKT L GDLKPIME YVEEELGQLL ATVHAGQEGA AIDYDNKAML AGILDHVGME VSDIAQVTAL GFPKSDPEAP LVEVGMGTLD AS KPVIIAI GHNVAGVTYI MDYMEDNNLT DKMEIGGLCC TAFDMTRYKR EDRKPPYAKI VGTISKELKV VRSGIPDVIV IDE QCVRAD LVEEGKKLKI PVIASNEKVM YGLPDRTNDD VDAIIEDIKT GKIPGCVMLD YEKLGELVPR LAMEMAPLRE GISA IPSDE EMASLVAKCV ACGECALACP EELDIPDAIQ AAKEGDFTAL DFLHDLCVGC RRCEQVCNKE IPILSVIDKA AQKAI AEEK GLVRAGRGQV SDAEIRAEGL NLVMGTTPGV IAIIGCANYP AGSKDVYRIA EEFLNRNYIV AVSGCSAMDI GMYKDA DGK TLYERFPGRF ERGNILNTGS CVSNSHISGT CHKVAAIFAG RNLSGNLAEI ADYTLNRVGA VGLAWGAYSQ KAAAIGT GC NMYGIPAVLG PHSGKYRRAL IAKTYDENKW KVYDSRNGSE LDIPPSPEFL ITTAETWQEA CVLLAKNCIR PSDNNMGR S IKLTHWIELS EKYLGVLPED WWKFVRHEAD LPLSRREELL KKLETEHGWE IDWKKKKIIS GPKIKFDVSS QPTNLKRLC KEA

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2

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Macromolecule #2: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2

MacromoleculeName: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina thermophila (archaea)
Molecular weightTheoretical: 18.587375 KDa
SequenceString:
MVDTTKNTKL FTSYGVKTSK AITTEVAAKL ISKAKRPLFV VGTGVLDPEL LDRAVKIAKA KNIPIAATGS SMPGFVDKDV NAKYINLHQ LGFYLTDPDW PGLDGNGNYD TIILLGHKKY YINQVLSAVK NFSDVKSISI DRNYIQNATM SFGNLSKADH I AALDEVID LL

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2

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Macromolecule #3: Acetyl-CoA decarbonylase/synthase complex subunit beta 2

MacromoleculeName: Acetyl-CoA decarbonylase/synthase complex subunit beta 2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: CO-methylating acetyl-CoA synthase
Source (natural)Organism: Methanosarcina thermophila (archaea)
Molecular weightTheoretical: 52.802227 KDa
SequenceString: MSEFPFEISP MFEGERVRKE GMFVELGGPK SLGLELVRAK PMDEIEDGKV TIVGPDLKDM EEGKTYPWAM IFHVGGELVE PDLESVIER RVHDFINYCQ GIMHLNQRYD VWMRISKDTA AKMDSFEPFG KAVMMLFKTE LPFIEKMQVT FYTDQAEVEK Q MAEAMEIF ...String:
MSEFPFEISP MFEGERVRKE GMFVELGGPK SLGLELVRAK PMDEIEDGKV TIVGPDLKDM EEGKTYPWAM IFHVGGELVE PDLESVIER RVHDFINYCQ GIMHLNQRYD VWMRISKDTA AKMDSFEPFG KAVMMLFKTE LPFIEKMQVT FYTDQAEVEK Q MAEAMEIF KARDARTKDL HDEDVDVFYG CTLCQSFAPT NVCVVSPDRV SLCGAINWFD GRAAAKVDPE GPQFAIEKGE LL DAKTGEY SGVNEVAKKL SSGEFDKIKL HSFFDAPHTS CGCFEVVGFY IPEVDGIGWV NREYQGMAPN GLGFSTMAGQ TGG GKQIVG FLGIGINYFY SPKFIQADGG WNRVVWLPSM LKEKIDEAIP DDMKDKIATE KDVTDIESLK TFLKEKNHPV VANW AAEAE EEEEEEEEEE EVAAEAAPMM MPAAGFQMPA MPAMPMMSGG AGGIKLTFKN AKITIDRMII SEKKEKK

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit beta 2

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 8 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: Fe(3)-Ni(1)-S(4) cluster

MacromoleculeName: Fe(3)-Ni(1)-S(4) cluster / type: ligand / ID: 5 / Number of copies: 2 / Formula: RQM
Molecular weightTheoretical: 410.333 Da
Chemical component information

ChemComp-RQM:
Fe(3)-Ni(1)-S(4) cluster

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Macromolecule #6: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #7: CARBON MONOXIDE

MacromoleculeName: CARBON MONOXIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: CMO
Molecular weightTheoretical: 28.01 Da
Chemical component information

ChemComp-CMO:
CARBON MONOXIDE

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Macromolecule #8: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
25.0 mMC7H15NO4SMOPS
25.0 mMNa2SO4Sodium sulfate
VitrificationCryogen name: ETHANE / Chamber humidity: 82 % / Chamber temperature: 298 K / Details: SPT Labtech chameleon plunger.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1124872
Startup modelType of model: NONE / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 33375
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial 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.
RefinementSpace: REAL / Overall B value: 76.1221 / Target criteria: Correlation coefficient
Output model

PDB-9c0s:
Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila

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