The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Di-Tryptophan targeting motif to the Delta-COP MHD domain
Functional site description:
COPI-coated vesicles mediate the essential retrograde trafficking from the Golgi to the endoplasmic reticulum (ER) and within the Golgi. The COPI vesicle coat consists of the coatomer and the small GTPase ADP ribosylation factor 1 (Arf1). The C-terminal μ Homology Domain (MHD) of the coatomer subunit δ-COP resides in the outermost layer of the coat, furthest from the vesicle membrane, thus being highly accessible to other factors. This MHD binds tryptophan-based motifs within the unstructured regions of coatomer assembly/tethering/disassembly factors, like the Dsl1 tether (yeasts) and the ArfGAPs (yeasts and mammals), that influence the life cycle of COPI-coated vesicles. Binding of such di-tryptophan motifs is unique to δ-COP MHD because the residues and the lengths of loops involved in binding are not conserved in other MHDs, like those of AP complexes, the TSET complex or muniscin family members FCHO1 and FCHO2.
ELM Description:
The δ-COP MHD binds with low micromolar KDs (∼10-40 μM) to di-tryptophan peptides with spacing of one to six residues embedded in negatively charged sequence. This suggests that the presence of two relatively closely spaced tryptophan side chains is the main determinant for δ-COP MHD binding (Suckling,2015), augmented by electrostatic interactions between charged and polar residues.
In the crystal structure (5FJZ), the WxW peptide from the Dsl1p lasso segment binds in an extended conformation with each tryptophan residue occupying a complementary hydrophobic pocket. Other motifs bound in a similar manner, including a WxxxW motif also from Dsl1p and the C-terminal WxxF motif of the yeast ArfGAP protein Gcs1p (5FJX; Suckling,2015). The binding site is comprised of δ-COP MHD strands 4 and 6 and the loop between strands 5 and 6. The identities of the residues and length of the interstrand loop at this site are well conserved from yeast to mammals. Importantly, di-Trp motif binding is unique to δ-COP because neither the residues nor the lengths of loops involved in binding are significantly conserved in other MHDs (Suckling,2015). Based on the verified instances and artificial peptides tested in mutational analyses (Cosson,1998; Rawet,2010; Suckling,2015) negatively charged residues are required in the vicinity of the specificity-determinant tryptophans: However, they are always present preceding the first Trp and these are included in the motif pattern.
The provided motif pattern may have a phylogenetic limitation: Based on mutation studies of the rat δ-COP - ArfGAP1 interaction (Rawet,2010), the tryptophan residues in ArfGAP1 could not be replaced by different aromatic or hydrophobic residues, whereas they can be for the δL peptide (C-terminal 17 residues of the YOR112Wp/Cex1p protein) in yeast (Cosson,1998).
Pattern: [DE]{1,3}.{0,2}W.{1,6}[WF]
Pattern Probability: 0.0005011
Present in taxon: Eukaryota
Interaction Domain:
Adap_comp_sub (PF00928) Adaptor complexes medium subunit family (Stochiometry: 1 : 1)
o See 5 Instances for LIG_deltaCOP1_diTrp_1
o Abstract
Eukaryotic cells contain many different organelles between which vesicles traffic cargo material. COPI-coated vesicles mediate essential, evolutionarily conserved retrograde trafficking pathways from the Golgi to the endoplasmic reticulum (ER) and within the Golgi. The COPI vesicle coat consists of two major components, coatomer and the small GTPase ADP ribosylation factor 1 (Arf1). Coatomer is a ∼600 kDa heteroheptameric complex consisting of two linked subcomplexes, the βγδζ-COP F-subcomplex and the αβ’ε-COP B-subcomplex, all conserved from yeast to humans (Suckling,2015). The life cycle of COPI-coated vesicles is controlled by essential assembly/disassembly factors. These include their specific multisubunit tethering complexes, SNARE complexes and the regulators of Arf1, the ArfGAPs. In the final stages of their life, COPI-coated vesicles dock with the ER via the Dsl1-tethering complex, complete uncoating, and finally undergo SNARE-mediated fusion with the ER membrane (Ren,2009; Suckling,2015).
The three-subunit yeast Dsl1 tethering complex forms an approximately 20 nm tall tower, with the Sec39 and Tip20 subunits together forming the base of the tower, interacting directly with two different ER SNAREs. At the tip of the tower is Dsl1, which contains a large, disordered lasso-like loop that can reach far from the ER membrane to capture COPI vesicles (Ren,2009). The interaction between tryptophan-based motifs surrounded by negatively charged residues within this lasso-like loop of Dsl1 with coatomer subunits δ and α (Reilly,2001; Andag,2003; Suckling,2015) have an important role in vesicle tethering.
In yeasts, the C-terminal μ homology domain (MHD) of δ-COP is responsible for recognising the tryptophan-based motifs of the Dsl1 lasso (5FJZ; Suckling,2015). This interaction does not seem to be preserved in mammals, as the mammalian Dsl1 homolog ZW10 lacks a tryptophan-rich lasso. However, the δ-COP MHD domain was also reported to interact with representatives of another class of COPI accessory factors, the ArfGAPs, Gcs1p in yeast (5FJX; Suckling,2015), and ArfGAP1 in mammals (Rawet,2010; Suckling,2015) through their C-terminal tryptophan motifs.
Based on the presence of similar Trp motifs in ER resident proteins, other potential interaction partners of δ-COP MHD were also proposed (Cex1p and Sec66 in yeast), however, the functional relevance of their potential association remains to be elucidated (Cosson,1998). Initially, the tryptophan-based motifs were proposed to function as ER localization/retrieval determinants (Cosson,1998).
The MHD of δ-COP is unique among other MHDs of vesicle coat adaptors in many regards: 1) While in clathrin-coated vesicle formation MHDs of clathrin adaptor AP complexes bind motifs within membrane-embedded cargos, the MHD of δ-COP mediates crucial interactions with vesicle tethering/(dis)assembly factors, which affect the life cycle of COPI vesicles. 2) Binding of di-tryptophan motifs is unique to δ-COP MHD because the residues and the lengths of loops involved in binding are not conserved in the MHDs of AP complexes or the TSET complex. Also, binding of the di-Trp motifs occurs at a site of δ-COP MHD that is completely different from the binding site of YxxΦ cargo motifs on AP MHDs (Suckling,2015). 3) A striking feature of the δ-COP MHD is its large negative electrostatic surface potential, which is conserved across species and is therefore presumably functionally important but is in marked contrast to the MHDs of AP1 and especially AP2, which are extremely positively charged. Since δ-COP MHD is actually on the outside of the coat, being the furthest part of the COPI coat from the membrane (Dodonova,2015), its high negative charge may contribute to the specificity of target membrane fusion of COPI-coated vesicles. It could inhibit close apposition and hence fusion with more negatively charged membranes such as the late Golgi/TGN, but not inhibit contact with the comparatively uncharged membranes of the cis-Golgi and ER (Suckling,2015). 4) EM tomography suggests that the δ-COP MHD motif binding site remains accessible in the hyper-open membrane-associated conformation, as well as in the assumed closed conformation of the coatomer F-subcomplex, indicating that it lacks a conformational switching mechanism to regulate ligand binding, like AP complexes. This again likely reflects the markedly different roles of the MHDs in COPI and AP complexes (Suckling,2015).
o 8 selected references:

o 14 GO-Terms:

o 5 Instances for LIG_deltaCOP1_diTrp_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q12453 CEX1
755 761 KGNVDGWDDDGDSDSWDTNW TP 6 Saccharomyces cerevisiae S288c
Q62848 Arfgap1
407 415 ATKKAAPSTAADEGWDNQNW TP 6 Rattus norvegicus (Norway rat)
P35197 GCS1
347 352 QKIDNNDKKNEQDEDKWDDF TP 3 Saccharomyces cerevisiae S288c
P53847 DSL1
452 459 KEPEEEENAWDEAWAIDENI TP 6 Saccharomyces cerevisiae S288c
P53847 DSL1
412 415 HNAVSKDDDWNWEVEDDDAD TP 7 Saccharomyces cerevisiae S288c
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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