The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
Adaptin binding Endosome-Lysosome-Basolateral sorting signals
Functional site description:
Endocytosis and/or vesicular sorting signals for membrane proteins. Depending on organism, cell type as well as the nature of the adaptin complex bound, they can target either to cell surface or to specific, internal membrane-bound organelles (endosomes, lysosomes, melanosomes, synaptic vesicles, etc.)

All these motifs are believed to bind to the sigma subunit of activated adaptin complexes (AP-1, AP-2 and AP-3). These clathrin-associated complexes are ancient and found in most eukaryotes. Dileucine motifs are variable (especially at their negatively charged positions and at the hydrophobic residues) and the various motif subtypes tend to have slightly different functions (Mattera,2011).

One should avoid confusing the adaptin sigma-binding classical dileucine motifs discussed here, and the GGA-binding lysosomal targeting motifs (sometimes also called dileucine motifs).
ELMs with same func. site: TRG_DiLeu_BaEn_1  TRG_DiLeu_BaEn_2  TRG_DiLeu_BaEn_3  TRG_DiLeu_BaEn_4  TRG_DiLeu_BaLyEn_6  TRG_DiLeu_LyEn_5 
ELM Description:
This relatively uncommon acidic dileucine-type motif features a phenylalanine at its first hydrophobic position (+5) instead of a leucine (Iverson,2005). Numbering is from the required Glu as +1. Motifs of this subtype are typically involved in basolateral sorting of membrane proteins in polarized epithelial cells (believed to be primarily driven by AP-1 association).

Since Phe-containing motifs do not appear to be suitable to act as a lysosomal signal, these variant motifs can also carry a proline before the two hydrophobic residues without the protein becoming lysosomal/late endosomal. Adding an additional negative charge (particularly glutamate) before its canonical glutamate (+1) would however strengthen them to the point where they would act mostly as a vesicular targeting signal (now considered to be a separate motif subtype in ELM) and therefore is disallowed for this functional variant.

Unfortunately, no detailed structural information is available on these motifs yet (as of 2021). Phe +5-containing dileucine motifs have not yet been described outside multicellular animals and it is questionable if they exist in fungi or plants.
Pattern: [^E]E...F[LIVM]
Pattern Probability: 0.0002451
Present in taxon: Metazoa
Interaction Domain:
Clat_adaptor_s (PF01217) Clathrin adaptor complex small chain (Stochiometry: 1 : 1)
o See 4 Instances for TRG_DiLeu_BaEn_2
o Abstract
Adaptin-binding acidic dileucine motifs and variants thereof occur almost exclusively on the cytosolic side of membrane proteins, mostly integral (transmembrane) proteins. In the latter, they are frequently located near the protein N- or C-termini, with relative proximity (within 10-100aa) to a transmembrane segment. These motifs bind directly to a highly conserved site located on the sigma subunits of adaptin complexes (adaptins AP1-4; Doray,2007; Kelly,2008). They serve to initiate clathrin-mediated endocytosis or protein sorting and can work synergistically with the adaptin mu subunit binding YxxPhi-type motifs (TRG_ENDOCYTIC_2). Sigma subunits of AP complexes differ slightly in their surface charge densities and binding groove geometry, allowing for both generic and selective interactions with protein partners.

In multicellular animals, AP1 targets its ligands from the trans-Golgi network to the cell membrane, mainly to the basolateral surface of polarized epithelial cells or somato-dendritic compartment of neurons (Nakatsu,2014). AP2 is chiefly involved in endocytosis of cell surface proteins and their trafficking to early or late endosomes. AP3 targets its ligands to the lysosome, late endosome or melanosome (or less commonly, to the axonal compartment of neurons), while the biological function of AP4 remains mostly unknown. In fungi and plants, dileucine motifs are often responsible for the vacuolar or tonoplast localization of proteins carrying these motifs.

Due to the similarity of the adaptin sigma subunits, variant dileucine motifs may have overlapping specificities, being capable of binding multiple adaptins. In many eukaryotes, AP3 appears to be a dominant partner, that drives permanent intracellular localization of ligands it can interact with, regardless of their binding to other adaptins. Unfortunately, the similarity of this motif to the GGA-binding dileucine motifs (that also target certain proteins to the late endosome or lysosome) has been the source of considerable confusion in the past.

The name of classical dileucine motifs stems from their preferred hydrophobic amino acids, although it is somewhat of a misnomer. In addition to the idealized ExxPL[LI] sequence, a multitude of relaxed motif variations are reported to exist, many of them still poorly characterized. The degree of relaxation seems to heavily influence the targeting properties of dileucine-like motifs (Sitaram,2012). Motifs that do not satisfy the optimal consensus tend to prefer adaptins other than AP3, hence they are more likely to be trafficked to the cell surface.
o 9 selected references:

o 12 GO-Terms:

o 4 Instances for TRG_DiLeu_BaEn_2
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
O15427 SLC16A3
MOT4_HUMAN
441 447 DSGVDLREVEHFLKAEPEKN TP 3 Homo sapiens (Human)
P09958 FURIN
FURIN_HUMAN
782 788 SEEDEGRGERTAFIKDQSAL TP 3 Homo sapiens (Human)
P20309 CHRM3
ACM3_HUMAN
275 281 QASGTEAETENFVHPTGSSR TP 3 Homo sapiens (Human)
Q9Y6R1 SLC4A4
S4A4_HUMAN
1052 1058 KIPMDIMEQQPFLSDSKPSD TP 3 Homo sapiens (Human)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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