9GYB

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

Summary for 9GYB

• Entry DOI: 10.2210/pdb9gyb/pdb
• Descriptor: Carbon monoxide dehydrogenase, IRON/SULFUR CLUSTER, Fe(3)-Ni(1)-S(4) cluster, ... (4 entities in total)
• Functional Keywords: carbon monoxide dehydrogenase redox nickel enzyme electron transfer, oxidoreductase
• Biological source: Rhodospirillum rubrum
• Total number of polymer chains: 6
• Total formula weight: 407217.56

Authors

Cavazza, C.,Contaldo, U. (deposition date: 2024-10-01, release date: 2025-02-19, Last modification date: 2025-04-02)

Primary citation

Contaldo, U.,Guigliarelli, B.,Perard, J.,Pichon, T.,Le Goff, A.,Cavazza, C.
Insights into the Role of the D-Cluster in [NiFe]-CODH from Rhodospirillum Rubrum.
Chemistry, 31:e202403648-e202403648, 2025

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. 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.

PubMed: 39912726
DOI: 10.1002/chem.202403648

Experimental method

X-RAY DIFFRACTION (2.9 Å)