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Structure paper

TitleCapturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 121, Issue 41, Page e2410995121, Year 2024
Publish dateOct 8, 2024
AuthorsAlison Biester / David A Grahame / Catherine L Drennan /
PubMed AbstractApproximately 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.
External linksProc Natl Acad Sci U S A / PubMed:39361653 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 3.3 Å
Structure data

45089

9c0q

EMDB-45089, PDB-9c0q:
Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermophila, specimen prepared on blot plunger
Method: EM (single particle) / Resolution: 3.3 Å

45090

9c0r

EMDB-45090, PDB-9c0r:
Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermophila, specimen prepared on chameleon plunger
Method: EM (single particle) / Resolution: 2.8 Å

45091

9c0s

EMDB-45091, PDB-9c0s:
Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila
Method: EM (single particle) / Resolution: 3.2 Å

45092

9c0t

EMDB-45092, PDB-9c0t:
Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) hexamer from Methanosarcina thermophila
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER

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

ChemComp-HOH:
WATER

ChemComp-F3S:
FE3-S4 CLUSTER

ChemComp-CMO:
CARBON MONOXIDE

ChemComp-NI:
NICKEL (II) ION

Source
  • methanosarcina thermophila (archaea)
KeywordsOXIDOREDUCTASE / CO-dehydrogenase / acetyl-CoA synthase / Methanosarcina thermophila

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