9G7I | pdb_00009g7i

Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with acetyl-Coenyzme A from Clostridium autoethanogenum

PDB DOI: https://doi.org/10.2210/pdb9G7I/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium autoethanogenum DSM 10061
Mutation(s): No

Deposited: 2024-07-21 Released: 2025-02-12
Deposition Author(s): Lemaire, O.N., Yin, M.D., Murphy, B.J., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.93 Å
R-Value Free:
0.220 (Depositor), 0.219 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Conformational dynamics of a multienzyme complex in anaerobic carbon fixation.

Yin, M.D., Lemaire, O.N., Rosas Jimenez, J.G., Belhamri, M., Shevchenko, A., Hummer, G., Wagner, T., Murphy, B.J.

(2025) Science 387: 498-504

PubMed: 39883773 Search on PubMed
DOI: https://doi.org/10.1126/science.adr9672
Primary Citation of Related Structures:
9FZY, 9FZZ, 9G00, 9G01, 9G02, 9G03, 9G7I

PubMed Abstract:
In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO ₂) 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 Clostridium autoethanogenum , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO ₂ 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 ₂ fixation in anaerobic organisms.

Organizational Affiliation

Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 297.7 kDa
Atom Count: 20,497
Modeled Residue Count: 2,661
Deposited Residue Count: 2,678
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CO-methylating acetyl-CoA synthase	A, D	708	Clostridium autoethanogenum DSM 10061	Mutation(s): 0 EC: 2.3.1.169
UniProt
Find proteins for F8TEQ9 (Clostridium autoethanogenum) Explore F8TEQ9 Go to UniProtKB: F8TEQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8TEQ9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase	B, C	631	Clostridium autoethanogenum DSM 10061	Mutation(s): 0 EC: 1.2.7.4
UniProt
Find proteins for F8TEP6 (Clostridium autoethanogenum) Explore F8TEP6 Go to UniProtKB: F8TEP6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8TEP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain SB [auth D] MOL2 format, chain SB [auth D] mmCIF format, chain SB [auth D]	SB [auth D]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain SB [auth D] Interactions & Density Focus chain SB [auth D]
XCC (Subject of Investigation/LOI) Query on XCC Download Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain CA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain CA [auth B]	CA [auth B], DB [auth C]	FE(4)-NI(1)-S(4) CLUSTER Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DB [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DB [auth C]
PE4 Query on PE4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain OB [auth D] SDF format, chain E [auth A] SDF format, chain BB [auth C] SDF format, chain AB [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain E [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain AB [auth C]	AB [auth C], BB [auth C], E [auth A], OB [auth D], Z [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain E [auth A] Focus chain OB [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain E [auth A] Focus chain OB [auth D] Focus chain Z [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain UB [auth D] MOL2 format, chain UB [auth D] mmCIF format, chain UB [auth D]	UB [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain UB [auth D] Interactions & Density Focus chain UB [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain RB [auth D] SDF format, chain L [auth A] SDF format, chain AA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain RB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain AA [auth B]	AA [auth B], L [auth A], RB [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain L [auth A] Focus chain RB [auth D] Interactions & Density Focus chain AA [auth B] Focus chain L [auth A] Focus chain RB [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain TB [auth D] SDF format, chain K [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain BA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain TB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain TB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] DA [auth B] EA [auth B] K [auth A] TB [auth D] BA [auth B], DA [auth B], EA [auth B], K [auth A], TB [auth D], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain K [auth A] Focus chain TB [auth D] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain K [auth A] Focus chain TB [auth D] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain ZB [auth D] SDF format, chain ZA [auth B] SDF format, chain YB [auth D] SDF format, chain YA [auth B] SDF format, chain XB [auth D] SDF format, chain XA [auth B] SDF format, chain X [auth A] SDF format, chain WA [auth B] SDF format, chain W [auth A] SDF format, chain VA [auth B] SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain NB [auth C] SDF format, chain NA [auth B] SDF format, chain MB [auth C] SDF format, chain MA [auth B] SDF format, chain LB [auth C] SDF format, chain LA [auth B] SDF format, chain KB [auth C] SDF format, chain JB [auth C] SDF format, chain J [auth A] SDF format, chain IB [auth C] SDF format, chain H [auth A] SDF format, chain CB [auth C] SDF format, chain AC [auth D] MOL2 format, chain ZB [auth D] MOL2 format, chain ZA [auth B] MOL2 format, chain YB [auth D] MOL2 format, chain YA [auth B] MOL2 format, chain XB [auth D] MOL2 format, chain XA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain AC [auth D] mmCIF format, chain ZB [auth D] mmCIF format, chain ZA [auth B] mmCIF format, chain YB [auth D] mmCIF format, chain YA [auth B] mmCIF format, chain XB [auth D] mmCIF format, chain XA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain AC [auth D]	AC [auth D] CB [auth C] H [auth A] IB [auth C] J [auth A] AC [auth D], CB [auth C], H [auth A], IB [auth C], J [auth A], JB [auth C], KB [auth C], LA [auth B], LB [auth C], MA [auth B], MB [auth C], NA [auth B], NB [auth C], OA [auth B], PA [auth B], QA [auth B], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], XB [auth D], YA [auth B], YB [auth D], ZA [auth B], ZB [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth D] Focus chain CB [auth C] Focus chain H [auth A] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth D] Focus chain YA [auth B] Focus chain YB [auth D] Focus chain ZA [auth B] Focus chain ZB [auth D] Interactions & Density Focus chain AC [auth D] Focus chain CB [auth C] Focus chain H [auth A] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth D] Focus chain YA [auth B] Focus chain YB [auth D] Focus chain ZA [auth B] Focus chain ZB [auth D]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain QB [auth D] SDF format, chain PB [auth D] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain PB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], PB [auth D], QB [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain PB [auth D] Focus chain QB [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain PB [auth D] Focus chain QB [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain WB [auth D] SDF format, chain VB [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain GB [auth C] SDF format, chain FB [auth C] SDF format, chain FA [auth B] SDF format, chain EB [auth C] MOL2 format, chain WB [auth D] MOL2 format, chain VB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth C] mmCIF format, chain WB [auth D] mmCIF format, chain VB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth C]	EB [auth C] FA [auth B] FB [auth C] GB [auth C] M [auth A] EB [auth C], FA [auth B], FB [auth C], GB [auth C], M [auth A], N [auth A], O [auth A], P [auth A], VB [auth D], WB [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain VB [auth D] Focus chain WB [auth D] Interactions & Density Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain VB [auth D] Focus chain WB [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HB [auth C] SDF format, chain HA [auth B] SDF format, chain GA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B]	GA [auth B] HA [auth B] HB [auth C] IA [auth B] JA [auth B] GA [auth B], HA [auth B], HB [auth C], IA [auth B], JA [auth B], KA [auth B], Q [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain Q [auth A] Focus chain R [auth A]