7B97 | pdb_00007b97

CooS-V with oxidized hybrid cluster by hydroxylamine for 30 min

PDB DOI: https://doi.org/10.2210/pdb7B97/pdb

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

Deposited: 2020-12-14 Released: 2022-01-12
Deposition Author(s): Jeoung, J.H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.171 (Depositor), 0.172 (DCC)
R-Value Work:
0.134 (Depositor), 0.135 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold.

Jeoung, J.H., Fesseler, J., Domnik, L., Klemke, F., Sinnreich, M., Teutloff, C., Dobbek, H.

(2022) Angew Chem Int Ed Engl 61: e202117000-e202117000

PubMed: 35133707 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202117000
Primary Citation Related Structures:
7B7Q, 7B7T, 7B95, 7B97, 7B9A

PubMed Abstract:
Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO ₂ to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe-cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS-V _Ch . Its structure reveals the typical CODH scaffold, but contains an iron-sulfur-oxo hybrid-cluster. Although closely related to true CODHs, CooS-V _Ch catalyzes neither CO oxidation, nor CO ₂ reduction. The active site of CooS-V _Ch undergoes a redox-dependent restructuring between a reduced [4Fe-3S]-cluster and an oxidized [4Fe-2S-S*-2O-2(H ₂ O)]-cluster. Hydroxylamine, a slow-turnover substrate of CooS-V _Ch , oxidizes the hybrid-cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O-cluster in place of the Ni,Fe-heterocubane-cluster of CODHs.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 138.52 kDa
Atom Count: 10,899
Modeled Residue Count: 1,258
Deposited Residue Count: 1,258
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase	A, B	629	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: cooSV, CHY_0034 EC: 1.2.7.4
UniProt
Find proteins for Q3AG28 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3AG28 Go to UniProtKB: Q3AG28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3AG28
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
T2N (Subject of Investigation/LOI) Query on T2N Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	3,5-dioxa-7-thia-1-thionia-2$l^{2},4$l^{2},6$l^{3},8$l^{2}-tetraferrabicyclo[4.2.0]octane Fe₄ O₂ S₂ ZZXANUDJVNRRAL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BU3 Query on BU3 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	G [auth A], H [auth A], L [auth B], M [auth B]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]
H2S (Subject of Investigation/LOI) Query on H2S Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]