5N76

Crystal structure of the apo-form of the CO dehydrogenase accessory protein CooT from Rhodospirillum rubrum

Summary for 5N76

• Entry DOI: 10.2210/pdb5n76/pdb
• Descriptor: CooT (2 entities in total)
• Functional Keywords: codh maturation, nickel-binding protein, anaerobic metabolism
• Biological source: Rhodospirillum rubrum
• Total number of polymer chains: 6
• Total formula weight: 42630.97

Authors

Timm, J.,Brochier-Armanet, C.,Perard, J.,Zambelli, B.,Ollagnier-de-Choudens, S.,Ciurli, S.,Cavazza, C. (deposition date: 2017-02-19, release date: 2017-05-10, Last modification date: 2024-10-23)

Primary citation

Timm, J.,Brochier-Armanet, C.,Perard, J.,Zambelli, B.,Ollagnier-de-Choudens, S.,Ciurli, S.,Cavazza, C.
The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein.
Metallomics, 9:575-583, 2017

PubMed Abstract: In Rhodospirillum rubrum, maturation of Carbon Monoxide Dehydrogenase (CODH) requires three accessory proteins, CooC, CooT and CooJ, dedicated to nickel insertion into the active site, which is constituted by a distorted [NiFeS] cubane coordinated with a mononuclear Fe site. CooC is an ATPase proposed to provide the energy required for the maturation process, while CooJ is described as a metallochaperone with 16 histidines and 2 cysteines at the C-terminus, likely involved in metal binding and/or storage. Prior to the present study, no information was available on CooT at the molecular level. Here, the X-ray structure of RrCooT was obtained, which revealed that this protein is a homodimer featuring a fold that resembles an Sm-like domain, suggesting a role in RNA metabolism that was however not supported by experimental observations. Biochemical and biophysical evidence based on circular dichroism spectroscopy, light scattering, isothermal titration calorimetry and site-directed mutagenesis showed that RrCooT specifically binds a single Ni(ii) per dimer, with a dissociation constant of 9 nM, through the pair of Cys2, highly conserved residues, located at the dimer interface. Despite its role in the activation of RrCODH in vivo, CooT was thought to be a unique protein, found only in R. rubrum, with an unclear function. In this study, we extended the biological impact of CooT, establishing that this protein is a member of a novel Ni(ii)-binding protein family with 111 homologues, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH.

PubMed: 28447092
DOI: 10.1039/c7mt00063d

Experimental method

X-RAY DIFFRACTION (1.9 Å)