The crystal structure of heme d1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo
Thomas Klünemann, Steffi Henke and Wulf Blankenfeldt [1]
Molecular Tour
NirC is a monoheme c-type cytochrome co-encoded with other proteins involved in nitrite reduction. It possesses the common fold hallmarked of three α-helices that surround a covalently attached heme. Its crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of eleven NirC chains in the asymmetric unit (PDB entry 6tp9). 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 NirC, the identification of conserved structural motifs in the monomer together with a comparison to similar proteins suggest an involvement of NirC in heme d1 biosynthesis.
The NirC monomer shown as a cartoon with residues at a maximum distance of 4 Å to the covalently attached heme presented as sticks:
Colours are based on sequence conservation as defined by Consurf. 
Depiction of the two different oligomerization states found in the crystal structure of NirC:
- 1st oligomerization state .
- .
- 2nd oligomerization state .
The residues of the hinge loop:
PDB reference: c-type cytochrome NirC 6tp9
References
- ↑ Klunemann T, Henke S, Blankenfeldt W. The crystal structure of the heme d1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo. Acta Crystallogr D Struct Biol. 2020 Apr 1;76(Pt 4):375-384. doi:, 10.1107/S2059798320003101. Epub 2020 Mar 25. PMID:32254062 doi:http://dx.doi.org/10.1107/S2059798320003101
