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:
The strict version of the dileucine motif is one of the most common variants, preferentially binding to AP-1 or AP-2 complexes. These motifs generally allow the proteins to reach the cell surface in multicellular animals, such as a basolateral localization in epithelia and/or reversible endocytosis into early endosomes. In neurons, such motifs are sometimes involved in somato-dendritic cell surface localization. The lack of a proline immediately preceding the two hydrophobic positions distinguishes these motifs from obligatory lysosomal (or axonal) targeting signals.

Although historically called acidic dileucine motifs, one or both hydrophobic positions can also be exchanged for hydrophobic amino acids other than leucine. On the other hand, dileucine motifs are more restrictive at their N-terminal ends. Contrary to earlier suggestions (Kelly,2008), it has now become clearer that dileucine motifs strongly prefer glutamate versus aspartate at their first position (an observation also supported by evolutionary conservation analyses). Structurally, this is due to the distance between the motif main chain and the charged surface of the sigma subunit, with Asp being too short (4P6Z_V; 4NEE_E; 6DFF_L; 6OWT_N). Conversely, Asp-carrying motifs need additional strengthening features (such as the above-mentioned proline) to remain functional. These divergent instances are now also treated as a separate motif subtype in ELM. Addition of one or more extra glutamates before the first Glu can also act as a strengthening feature, although it is not required for functionality if the hydrophobic contact points are otherwise optimal.

The classical 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 (Wang,2014). Thus, in these organisms, the motif appears to be functionally equivalent to other dileucine motif subtypes, including lysosomal targeting signals.
Pattern: E..[^P]L[LIVM]
Pattern Probability: 0.0009700
Present in taxon: Eukaryota
Interaction Domain:
Clat_adaptor_s (PF01217) Clathrin adaptor complex small chain (Stochiometry: 1 : 1)
o See 23 Instances for TRG_DiLeu_BaEn_1
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 10 selected references:

o 12 GO-Terms:

o 23 Instances for TRG_DiLeu_BaEn_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P11491 PHO8
PPB_YEAST
9 14 MTHTLPSEQTRLVPGSDSSS TP 5 Saccharomyces cerevisiae S288c
Q4JGV0 nef
Q4JGV0_SIV
190 195 SDEAQEDETHCLVHPAQTSQ TP 3 Simian immunodeficiency virus
1 
P03404 nef
NEF_HV1B1
160 165 VEEANKGENTSLLHPVSLHG TP 2 Human immunodeficiency virus type 1 BH10
1 
P04601 nef
NEF_HV1H2
160 165 IEEANKGENTSLLHPVSLHG TP 4 HIV-1 M:B_HXB2R
1 
P19554 vpu
VPU_HV1S1
63 68 ESEGDQEELSALVERGHLAP TP 5 Human immunodeficiency virus type 1 (SF162 ISOLATE)
1 
Q84WG0 NPF8.4
PTR26_ARATH
6 11 MASIDEERSLLEVEESLIQE TP 3 Arabidopsis thaliana (Thale cress)
Q9ZUA5 VIT1
VIT1_ARATH
16 21 TRISIEPEKQTLLDHHTEKH TP 5 Arabidopsis thaliana (Thale cress)
Q06328 YPQ2
YPQ2_YEAST
306 311 DSAAQLVTERTSLLSGETQT TP 3 Saccharomyces cerevisiae S288c
Q9Y2Q0 ATP8A1
AT8A1_HUMAN
1105 1110 VLGKSLTERAQLLKNVFKKN TP 3 Homo sapiens (Human)
Q62666 Slc18a3
VACHT_RAT
481 486 LLTRSRSERDVLLDEPPQGL TP 4 Rattus norvegicus (Norway rat)
P08033 Gjb1
CXB1_RAT
247 252 SPEYKQNEINKLLSEQDGSL TP 2 Rattus norvegicus (Norway rat)
P30205 Antigen WC1.1
WC11_BOVIN
1328 1333 LAEAVYEELDYLLTQKEGLG TP 2 Bos taurus (Cattle)
Q8BFW9 Slc2a12
GTR12_MOUSE
8 13 MVPVENTEGPNLLNQKGREA TP 3 Mus musculus (House mouse)
G5EGK5 cam-1
CAM1_CAEEL
541 546 GRVPPHVEMTSLLPSAQHLG TP 2 Caenorhabditis elegans
P50895 BCAM
BCAM_HUMAN
604 609 HSGSEQPEQTGLLMGGASGG TP 3 Homo sapiens (Human)
A0A1D5PL70 MCAM
A0A1D5PL70_CHICK
599 604 VKSDKLSEEAGLLQGANGEK TP 3 Gallus gallus (Chicken)
P51788 CLCN2
CLCN2_HUMAN
619 624 LALVESPESMILLGSIERSQ TP 4 Homo sapiens (Human)
P16070 CD44
CD44_HUMAN
708 713 GEASKSQEMVHLVNKESSET TP 4 Homo sapiens (Human)
P33527 ABCC1
MRP1_HUMAN
296 301 SKVDANEEVEALIVKSPQKE TP 3 Homo sapiens (Human)
P55087 AQP4
AQP4_HUMAN
288 293 EDNRSQVETDDLILKPGVVH TP 3 Homo sapiens (Human)
Q07954 LRP1
LRP1_HUMAN
4526 4531 HSLASTDEKRELLGRGPEDE TP 3 Homo sapiens (Human)
Q9UGH3 SLC23A2
S23A2_HUMAN
52 57 SSGEQDNEDTELMAIYTTEN TP 5 Homo sapiens (Human)
Q29983 MICA
MICA_HUMAN
339 344 KKKTSAAEGPELVSLQVLDQ TP 3 Homo sapiens (Human)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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