Fig. 5

Residues displaying subfamily-specific variation at the cytoplasmic slit. Residues of FNT channels forming the cytoplasmic slit representing the (A, B, C) closed and (D, E, F) open states. The cytoplasmic slit in the closed state is shown for (a) FocA (PDB ID: 3KLY; monomer A), (b) NirC-α (UniProt ID: I1XLF9) and (c) YfdC-α (UniProt ID: U1X6D4). The four residues forming the cytoplasmic slit in the closed state in PDB ID: 3KCU numbering are Leu-79 (TM2a), Leu-89 (Ω-loop), Thr-91 (Ω-loop) and Val-175 (TM4). Leu-89 and Thr-91 are almost invariant across all FNT channels. The hydrophobic character of Val-175 is maintained in all FNT subfamilies. Leu-79 is substituted by an aromatic residue in NirC-α and YfdC subfamilies. The cytoplasmic slit in the open state is formed by Leu-79 (TM2a), Leu-89 (Ω-loop), Phe-90 (Ω-loop), Asn-172 (TM4) and Val-175 (TM4) and is shown for (d) FocA (PDB ID: 3KLY; monomer E), (e) NirC-α (UniProt ID: I1XLF9) and (f) YfdC-α (UniProt ID: U1X6D4). Open states for NirC-α and YfdC-α were modeled similar to the procedure to model the open states of FocA channel described in the Methods section. Phe-90 shows absolute conservation in FocA subfamily and the aromatic character is nearly 100% conserved in YfdC-α subfamily. However, Asn-172, while showing absolute conservation in FocA and NirC-α subfamilies, is replaced by a Gly residue in YfdC subfamilies