9GYB | pdb_00009gyb

Crystal structure of the recombinant CODH from Rhodopspirillum rubrum produced in Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb9GYB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodospirillum rubrum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-01 Released: 2025-02-19
Deposition Author(s): Cavazza, C., Contaldo, U.
Funding Organization(s): French Alternative Energies and Atomic Energy Commission (CEA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.288 (Depositor), 0.288 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (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

Insights into the Role of the D-Cluster in [NiFe]-CODH from Rhodospirillum Rubrum.

Contaldo, U., Guigliarelli, B., Perard, J., Pichon, T., Le Goff, A., Cavazza, C.

(2025) Chemistry 31: e202403648-e202403648

PubMed: 39912726 Search on PubMed
DOI: https://doi.org/10.1002/chem.202403648
Primary Citation of Related Structures:
9GYB

PubMed Abstract:
The [NiFe]-CODH from Rhodospirillum rubrum contains [4Fe4S] clusters that allow electron transfer from the buried active sites to the protein surface. Among them, the role of the D-cluster, located at the dimer interface is still not fully understood. In this study, the removal of the D-cluster by site-directed mutagenesis revealed remarkable features in the behavior of the enzyme. Quantitative analysis and spectroscopic studies unveiled the suppression of D-cluster in the mutants and the influence on other metal cofactors. Furthermore, the CO oxidation activity in solution measured in the presence of methylviologen is almost completely abolished in the mutants. Conversely, direct electrochemistry at a functionalized carbon nanotube electrode shows that the mutants are still catalytically active reaching reduced but significant current densities of 0.7 mA cm-2. Moreover, the electroenzymatic activity towards oxygen is not affected by the removal of the D cluster. EPR studies reveal a remarkable change in the magnetic coupling between FeS clusters upon removal of the D-cluster, highlighting the effect of the location of this D-cluster at the dimer interface. It is noteworthy that in addition to its role as electron relay, the D-cluster appears to play an important role in the biosynthesis of the active site.

Organizational Affiliation

Université Grenoble Alpes: Universite Grenoble Alpes, LCBM, FRANCE.

Macromolecule Content

Total Structure Weight: 407.22 kDa
Atom Count: 27,316
Modeled Residue Count: 3,715
Deposited Residue Count: 3,834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase	A, B, C, D, E A, B, C, D, E, F	639	Rhodospirillum rubrum	Mutation(s): 0 Gene Names: cooS EC: 1.2.7.4
UniProt
Find proteins for P31896 (Rhodospirillum rubrum) Explore P31896 Go to UniProtKB: P31896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RQM Query on RQM Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain P [auth D] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain P [auth D] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain P [auth D] mmCIF format, chain H [auth A]	H [auth A] K [auth B] N [auth C] P [auth D] T [auth E] H [auth A], K [auth B], N [auth C], P [auth D], T [auth E], V [auth F]	Fe(3)-Ni(1)-S(4) cluster Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain V [auth F]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	G [auth A] I [auth B] J [auth B] L [auth C] M [auth C] G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], R [auth E], S [auth E], U [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]