Across families helix-helix packing motif V-G-x-L-[ACTV]-[AGT]-[IL]-[AGV]

Right-handed helix packing motif derived from fragments of size 10 in the Helix core region. The motif has been found mostly different transporters families, mainly in voltage-gated potassium channels (Pfam: PF02214), but also APC superfamily (CL0062), Major Facilitator superfamily (CL0015), Ion Channels (CL0030) etc. For a complete list of clans see below.

Structural description: The motif shows the conserved regular alpha-helix hydrogen bond pattern between main chain atoms in postions i,i+4. The backbone torsion angle pattern associated to the motif is illustrated below.

Functional annotation: The motif hits 214 transmembrane proteins in the Swiss-Prot database. The Swiss-Prot ids of the proteins carrying the motif are listed below.

The significant GO terms associated to the motif are the following: metal ion binding; ion channel activity; voltage-gated ion channel activity; aerobic respiration; copper ion binding; potassium ion binding; heme binding; cytochrome-c oxidase activity; mitochondrial electron transport chain. In all the pdb protein structures in the cluster, the motif is part of a long right-handed alpha-helix and it is involved in helix-helix packing with the helices in close proximity. The motif seems to be specific to transporters, especially potassium channels, rather than transmembrane receptors. It has been observed that pairs of helices in the transmembrane region can interact in few different ways and tend to interact over at least 10-residue segment (PMID:16954199). Furthermore, it is known that small residues like Ser, Gly, Ala and Thr (like the ones present in the following motif) are likely to be found at helix-helix interaction interfaces, playing a critical role in helix-helix packing and in general in maintaining the tertiary structure of helical membrane proteins (PMID:11518538).