8ON0 | pdb_00008on0

NI,FE-CODH -600mV state : 90 min Dioxygen Exposure

PDB DOI: https://doi.org/10.2210/pdb8ON0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2023-03-31 Released: 2023-12-06
Deposition Author(s): Basak, Y., Jeoung, J.-H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free:
0.157 (Depositor), 0.156 (DCC)
R-Value Work:
0.131 (Depositor), 0.131 (DCC)
R-Value Observed:
0.132 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Stepwise O 2 -Induced Rearrangement and Disassembly of the [NiFe 4 (OH)( mu 3 -S) 4 ] Active Site Cluster of CO Dehydrogenase.

Basak, Y., Jeoung, J.H., Domnik, L., Dobbek, H.

(2023) Angew Chem Int Ed Engl 62: e202305341-e202305341

PubMed: 37279092 Search on PubMed
DOI: https://doi.org/10.1002/anie.202305341
Primary Citation Related Structures:
8OMX, 8OMY, 8ON0, 8ON1, 8ON2, 8ON3

PubMed Abstract:
Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of carbon dioxide to carbon monoxide. CODHs are found in anaerobic microorganisms and can rapidly lose their activity when exposed to air. What causes the loss of activity is unclear. In this study, we analyzed the time-dependent structural changes induced by the presence of air on the metal centers of CODH-II. We show that inactivation is a multistep process. In a reversible step, the open coordination site on the Ni ion is blocked by a Ni,Fe-bridging μ-sulfido or chlorido ligand. Blocking this open coordination site with a cyanide ligand stabilizes the cluster against O ₂ -induced decomposition, indicating that O ₂ attacks at the Ni ion. In the subsequent irreversible phase, nickel is lost, the Fe ions rearrange and the sulfido ligands disappear. Our data are consistent with a reversible reductive reactivation mechanism to protect CODHs from transient over-oxidation.

Organizational Affiliation

Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 68 kDa
Atom Count: 5,516
Modeled Residue Count: 633
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase 2	A [auth X]	636	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: cooS2, cooSII, CHY_0085 EC: 1.2.7.4
UniProt
Find proteins for Q9F8A8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q9F8A8 Go to UniProtKB: Q9F8A8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9F8A8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X] mmCIF format, chain D [auth X]	D [auth X]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth X] SDF format, chain F [auth X] SDF format, chain G [auth X] SDF format, chain H [auth X] SDF format, chain I [auth X] SDF format, chain J [auth X] MOL2 format, chain E [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] MOL2 format, chain H [auth X] MOL2 format, chain I [auth X] MOL2 format, chain J [auth X] mmCIF format, chain E [auth X] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X] mmCIF format, chain H [auth X] mmCIF format, chain I [auth X] mmCIF format, chain J [auth X]	E [auth X] F [auth X] G [auth X] H [auth X] I [auth X] E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], J [auth X]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Interactions & Density Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X]
H2S (Subject of Investigation/LOI) Query on H2S Download:Ideal Coordinates CCD File SDF format, chain K [auth X] SDF format, chain L [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] mmCIF format, chain K [auth X] mmCIF format, chain L [auth X]	K [auth X], L [auth X]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain K [auth X] Focus chain L [auth X] Interactions & Density Focus chain K [auth X] Focus chain L [auth X]