Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains

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Abstract
Specific sorting signals direct transmembrane proteins to the compartments of the endosomal–lysosomal system1. Acidic-cluster-dileucine signals present within the cytoplasmic tails of sorting receptors, such as the cation-independent and cation-dependent mannose-6-phosphate receptors, are recognized by the GGA (Golgi-localized, γ-ear-containing, ADP-ribosylation-factor-binding) proteins2,3,4,5. The VHS (Vps27p, Hrs and STAM) domains6 of the GGA proteins are responsible for the highly specific recognition of these acidic-cluster-dileucine signals7,8,9,10. Here we report the structures of the VHS domain of human GGA3 complexed with signals from both mannose-6-phosphate receptors. The signals bind in an extended conformation to helices 6 and 8 of the VHS domain. The structures highlight an Asp residue separated by two residues from a dileucine sequence as critical recognition elements. The side chains of the Asp-X-X-Leu-Leu sequence interact with subsites consisting of one electropositive and two shallow hydrophobic pockets, respectively. The rigid spatial alignment of the three binding subsites leads to high specificity.