Structured-loop motif connecting two helices in subunit III of bc1 complex (Pfam: PF00033). This is the third complex in the electron transport chain and operates through a Q-cycle mechanism that couples electron transfer to generation of proton gradient that drives ATP synthesis (PMID: 14977419).

Structural description: The motif consists of a structured loop at the membrane-water interface, which contains a small interface helix, one turn long. The backbone torsion angle pattern associated to the motif is illustrated in fig. 1. Etc.. The motif, besides the standard alpha-helix hydrogen bond pattern between main chain atoms in postions i, i+4, shows a conserved pattern between main chain atoms in positions i, i+3 (irregular 3/10 alpha helix).

Functional annotation: The motif hits 909 transmembrane proteins in the Swiss-Prot database. The Swiss-Prot ids of the proteins carrying the motif are listed below: The GO terms associated to the motif are the following: mitochondrion, iron ion binding, transport, metal ion binding, oxidoreductase activity, mitochondrial electron transport chain, electron transport.

According to the interaction interface analysis carried out by using the SCOPPI database and our protein-ligand analysis in the PBD, the motif is part of the binding pocket of the heme group. In detail, the residues that non-covalently bind the heme group are Arg 101 and Ser 107 (pdb id: 1bcc, chain C and, equivalently, Arg 114 and Ser 120 in 2fyn, chain C and Arg 100, Ser 106 and Phe 109 in 2a06, chain C). According to the SCOPPI database, the motif is also found in proximity of the interaction interface with chain F (1bcc, 2a06 and, equivalently, G in 1kb9), a subunit of bc1 complex not directly involved in electron transfer, but playing a role in the assembly of the complex (PMID: 9651245).

The motif is novel and it doesn’t overlap with any known PROSITE pattern for the bc1 complex family.

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