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Structure paper

TitleConformational dynamics of a multienzyme complex in anaerobic carbon fixation.
Journal, issue, pagesScience, Vol. 387, Issue 6733, Page 498-504, Year 2025
Publish dateJan 31, 2025
AuthorsMax Dongsheng Yin / Olivier N Lemaire / José Guadalupe Rosas Jiménez / Mélissa Belhamri / Anna Shevchenko / Gerhard Hummer / Tristan Wagner / Bonnie J Murphy /
PubMed AbstractIn the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide ...In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). In this work, we present structural snapshots of the CODH/ACS from the gas-converting acetogen , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site, and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer, and protect the reaction intermediates. Altogether, the structures allow us to draw a detailed reaction mechanism of this enzyme, which is crucial for CO fixation in anaerobic organisms.
External linksScience / PubMed:39883773
MethodsEM (single particle) / X-ray diffraction
Resolution1.94 - 3.29 Å
Structure data

50897

9fzy

EMDB-50897, PDB-9fzy:
Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (composite structure, class 3A)
Method: EM (single particle) / Resolution: 2.71 Å

EMDB-50898: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (consensus map)
Method: EM (single particle) / Resolution: 1.94 Å

EMDB-50899: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (focused refinement, class 3A)
Method: EM (single particle) / Resolution: 2.71 Å

50900

9fzz

EMDB-50900, PDB-9fzz:
Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (composite structure, class 3B)
Method: EM (single particle) / Resolution: 2.65 Å

EMDB-50901: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (focused refinement, class 3B)
Method: EM (single particle) / Resolution: 2.65 Å

50902

9g00

EMDB-50902, PDB-9g00:
Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (composite structure, class 3Cb)
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-50903: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (focused refinement, class 3Cb)
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-50904: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (focused refinement, class 3Ca)
Method: EM (single particle) / Resolution: 2.78 Å

50905

9g01

EMDB-50905, PDB-9g01:
Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (composite structure, closed and CO-bound state)
Method: EM (single particle) / Resolution: 2.83 Å

EMDB-50906: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (focused refinement, closed and CO-bound state)
Method: EM (single particle) / Resolution: 2.83 Å

50907

9g02

EMDB-50907, PDB-9g02:
Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (composite structure, semi-extended state)
Method: EM (single particle) / Resolution: 3.29 Å

EMDB-50908: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (focused refinement, semi-extended state)
Method: EM (single particle) / Resolution: 3.29 Å

50909

9g03

EMDB-50909, PDB-9g03:
Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with ferredoxin (Clostridium autoethanogenum)
Method: EM (single particle) / Resolution: 2.1 Å

PDB-9g7i:
Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with acetyl-Coenyzme A from Clostridium autoethanogenum
Method: X-RAY DIFFRACTION / Resolution: 2.93 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-B12:
COBALAMIN

ChemComp-NI:
NICKEL (II) ION

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

ChemComp-CMO:
CARBON MONOXIDE

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-PE4:
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / precipitant*YM

ChemComp-GOL:
GLYCEROL

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-CA:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-XCC:
FE(4)-NI(1)-S(4) CLUSTER

ChemComp-ACO:
ACETYL COENZYME *A

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-HOH:
WATER

Source
  • clostridium autoethanogenum dsm 10061 (bacteria)
KeywordsOXIDOREDUCTASE / anaerobic CO2 fixation / acetyl-CoA synthesis / metalloenzyme / Wood-Ljungdahl pathway. / Carbon monoxide / acetyl-CoA / Wood-Ljungdahl pathway / C-cluster / A-cluster / gas channelling / acetogenic bacteria

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