The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Functional site description:
The LYPxL motif binds to the V-domain of eukaryotic Alix protein. Alix is associated with the ESCRT system, which is involved in endosomal sorting of membrane proteins. Many functional instances of the motif are known from retroviruses that use the host ESCRT system to bud from the cellular plasma membrane. In viruses, the LYPxL motif comprises a viral late assembly domain (L-domain). L-domains, located in viral Gag proteins, are required for the release of virions from the host cell. Mammalian host protein Syntenin has the LYPxL motif. In fungi such as yeasts, PACC and RIM101 have the motif.
ELMs with same func. site: LIG_LYPXL_L_2  LIG_LYPXL_S_1  LIG_LYPXL_SIV_4  LIG_LYPXL_yS_3 
ELM Description:
The yeast YPxL motif binds to a hydrophobic groove in the central V-domain of yeast proteins Bro1 and Rim20 (Alix_V domain-containing proteins), which are implicated in vacuolar transport and the pH response respectively. In the case of Rim20, it cleaves the Rim101 C-terminus by recognizing a YPxL motif downstream of the cleavage site. (Kimura,2014, Kimura,2015). As in the standard LYPxL motif, the binding is stabilized by both hydrophobic interactions as well as by a few important hydrogen bonds. In the motif of the yeast taxonomic grouping, the hydrophobic residue preceding the Tyrosine seems not to be strongly conserved. The first position of the yeast motif is highly conserved, tolerating solely tyrosine. It inserts into a deep hydrophobic pocket of Alix forming a hydrogen bond between the phenolic hydroxyl and a conserved aspartate (Zhai,2008). Proline at position three is also highly conserved. It leans against three hydrophobic residues on the Alix surface, with the binding centered on a conserved phenylalanine in ALIX (Baietti,2012). The yeast short version seems to allow a flexible spacing between a hydrophobic residue and the conserved tyrosine. The presence of modifiable or positively charged residues before the Tyrosine was also observed in alignments, but their conservation is not strong. The fourth position of the motif is most commonly represented by either leucine or isoleucine, but sequence alignments indicate other hydrophobic residues are also allowed.
Pattern: YP.[ILVM]
Pattern Probability: 0.0002195
Present in taxon: saccharomyceta
Interaction Domain:
ALIX_LYPXL_bnd (PF13949) ALIX V-shaped domain binding to HIV (Stochiometry: 1 : 1)
o See 2 Instances for LIG_LYPXL_yS_3
o Abstract
The LYPxL motif interacts with the cellular protein Alix (ALG2-interacting protein-1, or AIP1), which is associated with the Endosomal Sorting Complex Required for Transport (ESCRT). The ESCRT system is involved in the selective trafficking of membrane proteins to the lysosome by incorporating the membrane proteins into multivesicular bodies (MVBs). The final step in the biogenesis of MVBs is the ESCRT-mediated abscission of the cargo-containing vesicular membrane from the perimeter membrane (reviewed in Raiborg,2009). Some viruses have evolved strategies to hijack this process, which enables them to use ESCRT for the budding of viral particles from the host cell membrane.
Short peptide sequences within viral Gag proteins (encoding the structural proteins of the virus) are required for the separation of the virus from the host cell membrane. These sequences are called late assembly (L-) domains and mediate the interaction with components of ESCRT. So far, three different linear motifs in L-domains have been extensively studied: PTAP (LIG_PTAP_UEV_1), PPxY (LIG_WW_1) and LYPxL. These L-domains can function individually as well as cooperatively, and were demonstrated to be interchangeable between different viruses (reviewed in Demirov,2004).
In 1991, the importance of the PTAP residues of the caspid precursor for export of HIV-1 was reported (Gottlinger,1991). The LYPxL motif was then first characterized as a functional L-domain in EIAV by Puffer,1998. The link between the LYPxL motif and ESCRT was then established by identifying the ESCRT-associated protein Alix as a binding partner of LYPxL (Strack,2003). The recruitment of Alix is used to direct further members of ESCRT to the viral budding site, assembling the budding complex, which mediates the release of viral particles from the host cell. In this way, Alix acts as a bridging factor between ESCRT I and ESCRT III by binding both Tsg101 (ESCRT I) and CHMP4 (ESCRT III) (Pincetic,2009). LYPxL and PTAP are among the many short linear motifs that were first identified in viral proteins and only later in the regular cellular context.
The importance of the LYPxL motif in viral budding varies among different viruses, depending on the presence of other L-domains. LYPxL is essential for budding if it is the only L-domain motif present, as in EIAV. In contrast, other viruses such as HIV-1 possess more complex L-domains that can include two other ESCRT related motifs PTAP and PPxY that also contribute to efficient viral budding (Bieniasz,2006). In general, the role of the LYPxL L-domain in viral budding is considered to be minor compared to PPxY and PTAP (Dilley,2010).
In addition to viruses, the Apicomplexan parasite Toxoplasma gondii uses the YPxL motif during entry into the host cell: Two copies of LYPxL are present in the RON4 effector protein (Guerin,2017).
The LYPxL motif binds to a hydrophobic pocket located in the central V-domain of Alix. The binding is stabilized mostly by van-der-Waals interactions as well as a few hydrogen bonds. Within the LYPxL motif, two flanking hydrophobic residues as well as the tyrosine are considered to be crucial for the binding (Zhai,2008). The number of random residues tolerated at the fourth position is restricted to either one or three amino acids.
PacC, a transcription factor in Aspergillus nidulans, undergoes a two-step proteolytic activation as a response to alkaline pH. The Alix homologue PalA is required to direct a signalling protease to the cleavage sites of PacC. PacC contains two LYPxL motifs, one at each cleavage site to recruit PalA (Vincent,2003). The presence of LYPxL motifs in vertebrate cellular protein Syntenin allows its interaction with Alix, together with Syndecan, their complexes might ‘resemble’ viral budding and pertain to the formation of Intra-Luminal Vesicles (ILVs) and exosomes (Baietti,2012).
Until more cellular LYPxL motifs are identified, it will be difficult to fully assess the role of the motif in vesicular trafficking of the cell. Two variant motifs - short (LIG_LYPXL_S_1) and long (LIG_LYPXL_L_2) have been mainly identified in various viruses. Two new variant motifs short yeast (LIG_LYPXL_yS_3) and long SIV (LIG_LYPXL_SIV_4) based on new cellular and viral evidence provide a broader and flexible range of sequences for identifying additional V-Domain binders. All four variants are given a separate regular expression in ELM.
o 2 selected references:

o 8 GO-Terms:

o 2 Instances for LIG_LYPXL_yS_3
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P33400 RIM101
620 623 QNQMGTNSVRILTKYPKILV TP 2 Saccharomyces cerevisiae S288c
Q08003 RFU1
190 193 ARDEAYRLNYPELPRLTFST TP 6 Saccharomyces cerevisiae S288c
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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