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 LYPxL motif binds to a hydrophobic groove in the central V-domain of Alix (Lee,2007). The binding is stabilized by both hydrophobic interactions as well as by a few important hydrogen bonds. The 3D structure of the short LYPxL motif from EIAV in complex with Alix has been solved using X-ray crystallography (Zhai,2008; 2R03). The two hydrophobic residues flanking the Tyr at +2 make important hydrophobic contacts with Alix: Their substitution with alanine abrogates the binding. At position +1 a leucine is preferred or sometimes other hydrophobic residues occur. The second position of the motif is highly conserved, tolerating solely tyrosine. It inserts into a deep hydrophobic pocket of Alix forming a hydrogen bond between its phenolic hydroxyl and a conserved aspartate (Zhai,2008). Mutational analyses have shown that substitution of tyrosine to phenylalanine impedes binding. Proline at position +3 is also highly conserved. It leans against three hydrophobic residues on the Alix surface, with the binding centred on a conserved phenylalanine in Alix (Baietti,2012). The short version of the LYPxL motif contains one permissible amino acid at the fourth position. This spacing amino acid points away from the Alix surface and is therefore not involved in any direct interactions, explaining the low conservation of this position. Position +5 of the motif is most commonly adopted by either leucine or isoleucine, but alignments might indicate other hydrophobic residues are also allowed. The affinity of LYPDL in EIAV to Alix is 1.5 micromolar (Zhai,2008). The ELM derived pattern for the short version of the LYPxL motif is based on structure and alignment.
Pattern: [ILVMF]YP.[ILVMF]
Pattern Probability: 0.0000446
Present in taxon: Eukaryota
Interaction Domain:
ALIX_LYPXL_bnd (PF13949) ALIX V-shaped domain binding to HIV (Stochiometry: 1 : 1)
PDB Structure: 2R03
o See 18 Instances for LIG_LYPXL_S_1
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 11 selected references:

o 12 GO-Terms:

o 18 Instances for LIG_LYPXL_S_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
299 303 PIPASKGIYPNLDELRQTQE TP 4 Toxoplasma gondii
170 174 PIPASKGIYPSLDELRRSQE TP 3 Toxoplasma gondii
O00560 SDCBP
49 53 DGNLYPRLYPELSQYMGLSL TP 4 Homo sapiens (Human)
O00560 SDCBP
45 49 PIPHDGNLYPRLYPELSQYM TP 4 Homo sapiens (Human)
O00560 SDCBP
3 7 MSLYPSLEDLKVDKVIQAQT TP 4 Homo sapiens (Human)
P69732 gag
457 461 ETPQTQNLYPDLSEIKKEYN TP 12 Equine infectious anemia virus (ISOLATE WYOMING)
P03322 gag-pro
180 184 PPYVGSGLYPSLAGVGEQQG TP 1 Rous sarcoma virus - Prague C
Q00202 pacC
661 665 ESAEDSVMYPTLRGLDEDGD TP 1 Aspergillus nidulans
Q00202 pacC
454 458 PHESGSSMYPRLPSATDGMT TP 1 Aspergillus nidulans
Q83383 gag
128 132 QPPPRSALYPALTPSIKPRP TP 1 Murine leukemia virus
P03355 gag-pol
130 134 STPPRSSLYPALTPSLGAKP TP 3 Moloney murine leukemia virus
Q27ID9 gag
128 132 QPPSRSALYPALTPSIKSKP TP 1 Xenotropic MuLV-related virus VP62
P03331 gag
128 132 QPPPRSALYPALTPSIKPGP TP 1 Friend spleen focus-forming virus (isolate 502)
P03334 gag
130 134 STPPQSSLYPALTPSLGAKP TP 1 Moloney murine sarcoma virus
P21435 gag
128 132 GPPTRSSLYPALTPTKSPSP TP 1 HoMuLV murine leukemia virus
P26806 gag
130 134 STPPQSSLYPALTSPLNTKP TP 1 Friend murine leukemia virus (ISOLATE FB29)
P03340 gag
P29175 gag
128 132 QPPPRSALYPALTPSIKPRP TP 1 FBR murine osteosarcoma virus
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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