7ZKV

F231A variant of the CODH/ACS complex of C. hydrogenoformans

PDB DOI: https://doi.org/10.2210/pdb7ZKV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-04-13 Released: 2022-11-02
Deposition Author(s): Ruickoldt, J., Jeoung, J.-H., Basak, Y., Domnik, L., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.214
R-Value Work: 0.173
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Coupling CO2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis.

Ruickoldt, J., Jeoung, J.H., Rudolph, M.A., Lennartz, F., Kreibich, J., Schomacker, R., Dobbek, H.

(2024) Angew Chem Int Ed Engl : e202405120-e202405120

PubMed: 38743001 Search on PubMed
DOI: https://doi.org/10.1002/anie.202405120
Primary Citation of Related Structures:
7ZKV, 8CJA, 8CJB, 8CJC

PubMed Abstract:
The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO2 to the condensation of CO with a methyl-moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. Here, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover.

Organizational Affiliation

Humboldt-Universität zu Berlin, Biology, GERMANY.

Macromolecule Content

Total Structure Weight: 157.14 kDa
Atom Count: 11,973
Modelled Residue Count: 1,399
Deposited Residue Count: 1,399
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase	A	669	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 1 Gene Names: ciss_06270 EC: 1.2.7.4
UniProt
Find proteins for A0A1L8D0M5 (Carboxydothermus islandicus) Explore A0A1L8D0M5 Go to UniProtKB: A0A1L8D0M5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L8D0M5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CO-methylating acetyl-CoA synthase	B	730	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: acsB, CHY_1222 EC: 2.3.1.169
UniProt
Find proteins for Q3ACS4 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3ACS4 Go to UniProtKB: Q3ACS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3ACS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RQM (Subject of Investigation/LOI) Query on RQM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	Fe(3)-Ni(1)-S(4) cluster Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B]	D [auth A], E [auth A], K [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B]	J [auth B], L [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain J [auth B] Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
OH Query on OH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]