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:
Although relatively widespread and common in multicellular animals, dileucine motifs of this subtype (sometimes called PLL motifs) are quite poorly studied (Kozik,2010). The lack of a glutamate at +1 differentiates these motifs from the typical lysosomal targeting signals, but the presence of a proline is a shared feature. The lack of a glutamate likely weakens these motifs in that context, so they no longer act as an obligatory lysosomal targeting signal.

While interactions are based on similar structural principles, PLL motifs are quite heterogenous in terms of their function. They have a range of adaptin complexes they can associate with (AP-1, AP-2 and/or AP-3). This could be the result of variable amino acid composition at the motif N-termini: The strongest motifs approximate their lysosomal targeting counterparts, while suboptimal motifs might just serve as an endocytic or basolateral sorting signal. PLL motifs that have a positively charged amino acid (Arg or Lys) replacing the Glu +1 are considered especially weak but might still be able to bind the AP-2 complex due to structural reasons (Kelly,2008; 2JKR). As with the lysosomally targeting dileucine motifs, the proline preceding the two hydrophobic positions can also be exchanged for an arginine without loss of function.

In some cases, PLL motifs are part of phosphorylation-dependent switches, where a serine/threonine phosphorylation event creates the negative charge corresponding to the absent Glu at +1. As the modification is suggested to greatly increase adaptin binding, such conditional switches allow controlled endocytosis of certain proteins (Gibson,2000; Pitcher,1999).

This motif variant apparently also exists in diverse eukaryotes, including fungi and plants. The latter dileucine motifs were implicated in membrane protein sorting to vacuoles or tonoplasts. Thus, in these organisms they appear to be functionally equivalent to other dileucine motif subtypes.
Pattern: [^E]..[RP]L[LI]
Pattern Probability: 0.0010535
Present in taxon: Eukaryota
Interaction Domain:
Clat_adaptor_s (PF01217) Clathrin adaptor complex small chain (Stochiometry: 1 : 1)
o See 18 Instances for TRG_DiLeu_BaLyEn_6
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 18 Instances for TRG_DiLeu_BaLyEn_6
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P01730 CD4
CD4_HUMAN
434 439 RQAERMSQIKRLLSEKKTCQ TP 6 Homo sapiens (Human)
1 
Q94KI8 TPC1
TPC1_ARATH
1 6 MEDPLIGRDSLGGGGTDRVR TP 3 Arabidopsis thaliana (Thale cress)
Q8LG88 TDT
TDT_ARATH
14 19 TVAGSDDLKSPLLPVVHNDE TP 3 Arabidopsis thaliana (Thale cress)
Q9FN18 NRAMP4
NRAM4_ARATH
6 11 MSETDRERPLLASEERAYEE TP 3 Arabidopsis thaliana (Thale cress)
Q07549 SNA4
SNA4_YEAST
114 119 ARNVYPSVETPLLQGAAPHD TP 3 Saccharomyces cerevisiae S288c
P17643 TYRP1
TYRP1_HUMAN
510 515 ARRSMDEANQPLLTDQYQCY TP 3 Homo sapiens (Human)
Q9NRA2 SLC17A5
S17A5_HUMAN
18 23 NDGEESTDRTPLLPGAPRAE TP 3 Homo sapiens (Human)
Q01705 Notch1
NOTC1_MOUSE
2098 2103 AQERMHHDIVRLLDEYNLVR TP 3 Mus musculus (House mouse)
P41180 CASR
CASR_HUMAN
1009 1014 KSSDTLTRHEPLLPLQCGET TP 3 Homo sapiens (Human)
P41143 OPRD1
OPRD_HUMAN
241 246 GLMLLRLRSVRLLSGSKEKD U 3 Homo sapiens (Human)
Q91CB6 E3 45.8 K
Q91CB6_ADE09
400 405 CRKRPRSYNHMVDPLLSFSY U 3 Human adenovirus 9
P12830 CDH1
CADH1_HUMAN
737 742 FLRRRAVVKEPLLPPEDDTR U 3 Homo sapiens (Human)
Q01814 ATP2B2
AT2B2_HUMAN
1180 1185 FRIEDSQPHIPLIDDTDLEE TP 3 Homo sapiens (Human)
P20020 ATP2B1
AT2B1_HUMAN
1157 1162 FRIEDSEPHIPLIDDTDAED TP 3 Homo sapiens (Human)
P55011 SLC12A2
S12A2_HUMAN
985 990 EEEDGKTATQPLLKKESKGP TP 3 Homo sapiens (Human)
Q9ULH4 LRFN2
LRFN2_HUMAN
694 699 SARGHHSDREPLLGPPAARA TP 2 Homo sapiens (Human)
Q9EQJ0 Tpcn1
TPC1_MOUSE
7 12 MAVSLDDDVPLILTLDEAES TP 3 Mus musculus (House mouse)
P40189 IL6ST
IL6RB_HUMAN
782 787 QVFSRSESTQPLLDSEERPE TP 2 Homo sapiens (Human)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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