Family specific motif in helix A of subunit III (PMID: 9565029) of Ubiquinol-cytochrome-c oxidoreductase (bc1 complex, Pfam: PF00033). The bc1 complex is a central component of the energy-transducing respiratory chain and operates through a Q-cycle mechanism that couples electron transfer to generation of proton gradient that drives ATP synthesis (PMID: 14977419). The motif is involved in non-covalent interaction with the heme group.

Structural description: The motif shows the regular alpha-helix hydrogen bond pattern, between main chain atoms in positions i, i+4, besides a highly conserved hydrogen bond between Thr 48 side chain and Gln 45 main chain atom or main chain atom of amino acid in position 44 (pdb_id: 1bcc, chain C). The backbone torsion angle patter associated to the motif is illustrated below (set an internal link).

Functional annotation: The motif hits 872 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 , embedded in the membrane helix core, is part of the bH heme binding scaffold. In detail, the residues that non-covalently bind the heme group are Gln45, Gly49, Leu50 in the 1bcc structure, chain C. It has been shown by site-directed mutagenesis studies of highly conserved residues in cytochrome b subunit that, when from the bc1 complex of Rhodobacter spheroides Gly 48 (respectively Gly 49 in 1bcc, chain C), is mutated to Asp or Val, the function of the protein is affected as it leads to the formation of a bc1 complex with modified cytochromes bH and bL and a dysfunctional quinone reductase site (PMID: 1313421). An Ala mutation is tolerated at this positionand this brings to the hypothesis that a small residue is important for heme packing. It can be speculated the whole motif, highly involved in interactions with the heme group, is important for accommodating the heme-packing in the four-helical bundle.

The motif is novel and it doesn't overlap with any know PROSITE pattern for the bc1 complex family. A non-significant overlap (60% similarity score) is observed with the Prenyl group binding site (CAAX box) signature pattern in the PROSITE database (similarity sore) is observed with the Prenyl group binding site (CAAX box) signature pattern in the PROSITE database (PS00294).

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