Abstract.Copper is essential for life but toxic, therefore all organisms control tightly its intracellular abundance. Bacteria have indeed whole operons devoted to copper resistance, with genes that code for efflux pumps, oxidases, etc. Recently, the CopM protein of the CopMRS operon was described as a novel important element for copper tolerance in Synechocystis. This protein consists of a domain of unknown function, and was proposed to act as a periplasmic/extracellular copper binder. This work describes a bioinformatic study of CopM including structural models based on homology modeling and on residue coevolution, to help expand on its recent biochemical characterization. The protein is predicted to be periplasmic but membrane-anchored, not secreted. Two disordered regions are predicted, both possibly involved in protein-protein interactions. The 3D models disclose a 4-helix bundle with several potential copper-binding sites, most of them largely buried inside the bundle lumen. Some of the predicted copper-binding sites involve residues from the disordered regions, suggesting they could gain structure upon copper binding and thus possibly modulate the interactions they mediate. All models are provided as PDB files in the Supporting Information and can be visualized online at http://lucianoabriata.altervista.org/modelshome.html Note (January 2017): Recent X-ray structures of apo, copper-and silver-bound CopM are < 3Å RMSD away from the models, and reveal metal-dependent structural flexibility (Zhao et al Acta Crystallogr D Struct Biol. 2016)

The soluble domain of cytochrome c oxidase subunit II (COX2), located in the outer side of the inner mitochondrial membrane, contains a binuclear copper site (CuA) through which electrons flow from cytochrome c to the core of the oxidase where oxygen reduction takes place. Being COX2 encoded in the mitochondrial genome, newly synthesized protein undergoes maturation steps in which it is translocated through and inserted into the inner mitochondrial membrane, and copper ions are loaded to form the CuA site. These steps are ensured by several protein factors in a complex pathway that is not fully understood, including copper-loading and disulfide-reduction proteins plus chaperones that assist proper membrane insertion. While the structure and function of copper-loading and disulfide-reducing proteins Sco1 and Sco2 have been quite studied at atomistic level, the latest biological studies have uncovered roles for other proteins that are not yet much understood at the structural level. In particular, recent experiments showed that membrane protein COX18 is a membrane-protein insertase for COX2, whereas membrane protein COX20 is a chaperone that stabilizes COX2 during translocation through the inner mitochondrial membrane, and soluble protein COA6 is part of the copper-loading pathway in conjunction with Sco1 and Sco2. This work reports structural models for COX18, COX20 and COA6, built judiciously from homology modeling, contact prediction-based modeling and transmembrane helix predictions, while considering the underlying biology. Implications and limitations of the models are discussed, and possible experimental routes to pursue are proposed. All models are provided as PyMOL sessions in the Supporting Information and can be visualized online at