The crystal structure of heme d1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo

Abstract

Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three -helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their -helices, which is often referred to as 3D domain swapping. Here, we have determined the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa. Crystals diffracted anisotropically to a maximum resolution of 2.12 [A] (spherical resolution 2.83 [A]) and initial phases were obtained by Fe-SAD phasing, revealing the presence of eleven NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D-domain-swapped dimers, one showing pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison to similar proteins may offer new leads to unravel the unknown function of NirC. SynopsisThe crystal structure of the c-type cytochrome NirC from Pseudomonas aeruginosa has been determined and reveals the simultaneous presence of monomers and 3D-domain-swapped dimers in the same asymmetric unit.