The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
Atg8 protein family ligands
Functional site description:
The autophagy-related protein Atg8 and its homologues LC3 and GABARAP play an important role in selective autophagy. During autophagy, Atg8 proteins get directly conjugated to phosphatidylethanolamine (PE) lipids to mediate membrane fusion events involved in autophagosome biogenesis such as phagophore formation and elongation. In addition, different Atg8 protein family members can recruit specific adaptors bound to ubiquitylated proteins, organelles or pathogens for degradation. Many of these adaptor proteins contain an LC3-interacting region (LIR) that mediates binding to Atg8 and Atg8-related proteins. These LIR:Atg8/LC3/GABARAP interactions are essential for cellular cell homeostasis as well as the control of intra- and extracellular stress conditions.
ELMs with same func. site: LIG_LIR_Apic_2  LIG_LIR_Gen_1  LIG_LIR_LC3C_4  LIG_LIR_Nem_3 
ELM Description:
The core of the LIR motif is defined by four amino acids and adopts a β-strand conformation that binds by β-augmentation, forming an intermolecular parallel β-sheet with the second β-strand of Atg8 protein family members (Rogov,2014). There is an absolute requirement for an aromatic residue at the N-terminal side of the LIR core and a large, hydrophobic residue at the C-terminal side. Structural studies have revealed that the side chain of the aromatic residue of the LIR motif binds deeply in HP1 whereas the hydrophobic residue docks to HP2 (2ZJD; Ichimura,2008). Position +2 in the core is solvent accessible and aromatic residues are not favoured. The presence of positive charges in the binding domain also restricts the +2 position to not-positively charged residues. The fixed distance from HP1 to HP2 makes it inadequate for a tiny residue or a Pro at +2 and +3 positions. The core motif is generally preceded by a varying number of acidic residues or by Ser or Thr residues that can be phosphorylated to incorporate a negative charge. These residues commonly occur within three positions N-terminal to the core motif. The negative charge of these acidic or phosphorylated residues has been shown to strengthen the LIR:Atg8/LC3/GABARAP interaction (Rogov,2013). Additional acidic residues or Ser/Thr phosphorylation sites that strengthen the interaction are sometimes observed in the positions between the aromatic (+1) and hydrophobic (+4) residue. A Trp residue is energetically favoured for this interaction over a Tyr or Phe residue, but the lower binding affinity can be compensated by electrostatic interactions between acidic residues or Ser/Thr phosphorylation sites of the LIR motif and basic residues in the N-terminal arm of the Atg8 homologues (Wild,2013). Analysis of current known structures indicates that the motif can be located at the C-terminus of the protein or be followed by a particular range of acidic or not residues immediately, or up to four positions, after the core.

Pattern: [EDST].{0,2}[WFY][^RKPGWFY][^PG][ILVFM]((.{0,4}[PLAFIVMY])|($)|(.{0,3}[ED]))
Pattern Probability: 0.0036312
Present in taxon: Eukaryota
Not represented in taxon: Nematoda
Interaction Domain:
Atg8 (PF02991) Autophagy protein Atg8 ubiquitin like (Stochiometry: 1 : 1)
PDB Structure: 2Z0E
o See 54 Instances for LIG_LIR_Gen_1
o Abstract
Macroautophagy is an evolutionary conserved degradation process that targets macromolecules, organelles and intracellular pathogens and is of vital importance for cellular homeostasis. Many of the proteins involved in autophagy were first identified and named in yeast. In this process, a double membrane structure called the phagophore forms and expands to form a double-membrane vesicle, the autophagosome. Autophagosomes then sequester cargo and eventually fuse with the vacuole in yeast or the lysosome in higher eukaryotes in order to degrade their content (Mizushima,2011). Several autophagy-related proteins (Atgs) are required for the formation of the autophagosome and they are highly conserved in Eukaryotes. Among these Atg proteins are the yeast autophagy protein Atg8 and its vertebrate homologues which are ubiquitously expressed in all tissues. An upregulation of Atg8 proteins can be observed under various stress conditions (Shpilka,2011). After its translation, the carboxy-terminal region of Atg8 is cleaved in order to expose a glycine residue. Atg8 is then processed by an ubiquitin-like conjugation machinery, which directly conjugates it via its exposed glycine to a PE (phosphatidylethanolamine) lipid. This enables Atg8 to be involved both in cargo recruitment into autophagosomes and the formation and elongation of the autophagosome (Johansen,2011).
In contrast to yeast and other fungal species, which have only a single Atg8 protein (P38182), multicellular animals, plants and some protists have several Atg8 homologues. These can be grouped into two subfamilies: the microtubule-associated protein 1 light-chain 3 (MAP1LC3 or LC3) with its paralogous variants LC3A (Q9H492), LC3B (Q9GZQ8) and LC3C (Q9BXW4), with two spliced isoforms of LC3A, and the γ-aminobutyrate receptor-associated paralogous proteins including GABARAP (O95166), GABARAPL-1 (Q9H0R8) and GABARAPL-2 (P60520). Proteins binding to the Atg8 protein family typically possess a short hydrophobic LC3-Interacting Region (LIR) motif, which is often also referred to as Atg8-family Interacting Motif (AIM) in yeast. The LIR is required for these proteins to bind Atg8 and its homologues. Proteins containing LIR motifs include cargo receptors, members of the basal autophagy apparatus, proteins associated with vesicles and of their transport, Rab GTPase-activating proteins (GAPs) and specific signalling proteins that are degraded by selective autophagy. They represent an essential part of autophagosome formation, transport and maturation (Birgisdottir,2013).
Proteins belonging to the Atg8 family have a C-terminal domain (PF02991) belonging to the large ubiquitin-like (UBL) domain superclass which consists of a four-stranded β-sheet wrapped around a central α-helix. The hydrophobic residues of the central α-helix and β-strand 2 of the UBL core form a hydrophobic pocket (HP2). Preceding and extending the UBL core is an N-terminal arm with two α-helices. This N-terminal subdomain varies among the different Atg8 subfamilies. It is packed onto the core UBL and forms another deep hydrophobic pocket (HP1) (2KWC; Kumeta,2010). The LIR docking site is located at the interface of the UBL core and the N-terminal arm and consists of the two hydrophobic pockets HP1 and HP2.
When cells are invaded by pathogenic bacteria, autophagy is used to capture and subsequently eliminate the invader in conjunction with the lysosome: this process is also called xenophagy. Pathogens have been found to counteract this process by evolving mechanisms to evade or abuse autophagy. Legionella pneumophila secretes the protease RavZ to irreversibly deconjugate LC3-PE by cleaving the Glycine-containing C-terminal region. In order to recognize its target protein, RavZ uses three mimics of the LIR motif to bind to up to two LC3 molecules (Kwon,2017). A secreted protein from the oomycete Phytophthora infestans binds to the autophagy-related protein ATG8CL from potato outcompeting with the host cargo receptor affecting the plant defense (Dagdas,2016).
Viruses also interact with the autophagy system. Influenza A virus requires the presence of LC3 at the plasma membrane during virus budding to form filamentous virions and, ultimately, for enhanced virion stability. The relocalization of LC3 depends on a LIR motif in the cytoplasmic tail of Matrix 2 ion-channel protein (Beale,2014). Coronavirus, including SARS-CoV-2, proteins accumulate or prevent the efficient formation of autophagosomes (Koepke,2021): However, at time of writing, no LIR motif has been identified in coronavirus proteins.
LIR motifs described in nematodes are less specific, as they accept a wider range of residues after the aromatic residue including tiny residues at the +2 position and Tyr at +4 of the core. Likewise, Apicomplexa LIRs use a Pro residue at the +4 position which is not observed in other eukaryotes. For these reasons, two non-canonical classes exist: LIG_LIR_Apic_2 and LIG_LIR_Nem_3.
A structural difference in LC3C homologues reduces the exposure of HP2 compared to other Atg8 homologues, this restricts the core to a 3-amino acid core and is described in the ELM class LIG_LIR_LC3C_4.
o 8 selected references:

o 5 GO-Terms:

o 54 Instances for LIG_LIR_Gen_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
W6PPR4 Ank3
W6PPR4_MOUSE
1987 1996 HSPEDDWTEFSSEEIREARQ TP 4 Mus musculus (House mouse) [new]
1 
Q14596 NBR1
NBR1_HUMAN
730 740 SASSEDYIIILPECFDTSRP TP 6 Homo sapiens (Human) [new]
7 
Q96CV9 OPTN
OPTN_HUMAN
175 184 SSGSSEDSFVEIRMAEGEAE TP 12 Homo sapiens (Human) [new]
5 
P40458 ATG32
ATG32_YEAST
85 94 DSISGSWQAIQPLDLGASFI TP 3 Saccharomyces cerevisiae S288c [new]
1 
Q8MQJ7 Atg1
Q8MQJ7_DROME
390 399 HEDSDDFVLVPKNLPEDQRQ TP 3 Drosophila melanogaster (Fruit fly) [new]
1 
Q92609 TBC1D5
TBCD5_HUMAN
58 64 FNSYRKEWEELFVNNNYLAT TP 5 Homo sapiens (Human) [new]
3 
Q92609 TBC1D5
TBCD5_HUMAN
785 795 SPDDDSSKDSGFTIVSPLDI TP 5 Homo sapiens (Human) [new]
3 
Q00610 CLTC
CLH1_HUMAN
511 522 KVGYTPDWIFLLRNVMRISP TP 3 Homo sapiens (Human) [new]
1 
P40344 ATG3
ATG3_YEAST
269 277 LDGVGDWEDLQDDIDDSLRV TP 4 Saccharomyces cerevisiae S288c [new]
1 
Q9Y4P1 ATG4B
ATG4B_HUMAN
10 20 LTYDTLRFAEFEDFPETSEP TP 2 Homo sapiens (Human) [new]
1 
Q3MII6 TBC1D25
TBC25_HUMAN
135 144 SPLLEDWDIISPKDVIGSDV TP 4 Homo sapiens (Human) [new]
3 
Q12983 BNIP3
BNIP3_HUMAN
82 88 EESLQGSWVELHFSNNGNGG TP 5 Homo sapiens (Human) [new]
2 
Q8IYT8 ULK2
ULK2_HUMAN
351 360 SSCDTDDFVLVPHNISSDHS TP 1 Homo sapiens (Human) [new]
6 
Q9BQS8 FYCO1
FYCO1_HUMAN
1277 1288 RPPDDAVFDIITDEELCQIQ TP 6 Homo sapiens (Human) [new]
6 
O75143 ATG13
ATG13_HUMAN
443 452 GNTHDDFVMIDFKPAFSKDD TP 7 Homo sapiens (Human) [new]
6 
Q5ZUV9 lpg1683
Q5ZUV9_LEGPH
434 443 DDTIDDFVTIEKDELFDVPD TP 12 Legionella pneumophila subsp. pneumophila str. Philadelphia 1 [new]
1 
Q99442 SEC62
SEC62_HUMAN
362 371 SGNGNDFEMITKEELEQQTD TP 4 Homo sapiens (Human) [new]
6 
Q6ZNE5 ATG14
BAKOR_HUMAN
434 443 TDLGTDWENLPSPRFCDIPS TP 5 Homo sapiens (Human) [new]
5 
O75385 ULK1
ULK1_HUMAN
356 365 SCDTDDFVMVPAQFPGDLVA TP 5 Homo sapiens (Human) [new]
6 
Q5ZUV9 lpg1683
Q5ZUV9_LEGPH
28 36 ESDIDEFDLLEGDEKLPGDS TP 14 Legionella pneumophila subsp. pneumophila str. Philadelphia 1 [new]
1 
Q5ZUV9 lpg1683
Q5ZUV9_LEGPH
15 23 KLIVDEFEELGEQESDIDEF TP 9 Legionella pneumophila subsp. pneumophila str. Philadelphia 1 [new]
1 
Q15154-5 PCM1
PCM1_HUMAN
1954 1963 KSDEEDFVKVEDLPLKLTIY TP 9 Homo sapiens (Human) [new]
6 
Q9C0C7-3 AMBRA1
AMRA1_HUMAN
1017 1028 NSGVEYYWDQLNETVFTVHS TP 4 Homo sapiens (Human) [new]
6 
Q9Y4G2 PLEKHM1
PKHM1_HUMAN
634 641 RPQQEDEWVNVQYPDQPEEP TP 6 Homo sapiens (Human) [new]
6 
Q9H6L5-1 RETREG1
RETR1_HUMAN
454 463 TEEGDDFELLDQSELDQIES TP 6 Homo sapiens (Human) [new]
5 
Q9UQF2 MAPK8IP1
JIP1_HUMAN
334 342 ISEEEEGFDCLSSPERAEPP TP 3 Homo sapiens (Human) [new]
Q9GYV5 key
NEMO_DROME
6 14 MSDEESFVILGSSPCSSLMP TP 3 Drosophila melanogaster (Fruit fly) [new]
1 
Q9Y6I9 TEX264
TX264_HUMAN
271 278 ESGASGSSFEELDLEGEGPL TP 2 Homo sapiens (Human) [new]
1 
O15040 TECPR2
TCPR2_HUMAN
1407 1411 KSSQAAMPHPEDLEDEWEVI TP 8 Homo sapiens (Human) [new]
5 
Q99325 ATG40
ATG40_YEAST
241 249 TEFPNDYDFMEDILDETTEL TP 4 Saccharomyces cerevisiae S288c [new]
1 
Q96A56-1 TP53INP1
T53I1_HUMAN
30 37 NEKEDDEWILVDFIDTCTGF FP 5 Homo sapiens (Human) [new]
Q95V81 seq
Q95V81_DROME
303 311 EHEYEEYQVIKAEVEAEAAE TP 3 Drosophila melanogaster (Fruit fly) [new]
1 
Q8TDY2 RB1CC1
RBCC1_HUMAN
701 710 DAHTFDFETIPHPNIEQTIH TP 3 Homo sapiens (Human) [new]
6 
Q8NEB9 PIK3C3
PK3C3_HUMAN
248 258 SPILTSFELVKVPDPQMSME U 5 Homo sapiens (Human) [new]
5 
Q8IZQ1 WDFY3
WDFY3_HUMAN
3344 3351 LSLDEKDGFIFVNYSEGQTR TP 10 Homo sapiens (Human) [new]
4 
Q7Z6L1 TECPR1
TCPR1_HUMAN
173 179 RRYKSRDIWAKIPSKDDPKE TP 5 Homo sapiens (Human) [new]
1 
Q14457 BECN1
BECN1_HUMAN
96 103 STESANSFTLIGEASDGGTM TP 5 Homo sapiens (Human) [new]
5 
Q14318 FKBP8
FKBP8_HUMAN
23 30 GVPPLEDFEVLDGVEDAEGE TP 5 Homo sapiens (Human) [new]
1 
Q13501 SQSTM1
SQSTM_HUMAN
335 346 CSGGDDDWTHLSSKEVDPST TP 1 Homo sapiens (Human) [new]
6 
Q01484 ANK2
ANK2_HUMAN
1591 1600 GLVEEEWVIVSDEEIEEARQ TP 3 Homo sapiens (Human) [new]
2 
P59017 Bcl2l13
B2L13_MOUSE
272 280 SLGPESWQQIAMDPEEVKSL TP 3 Mus musculus (House mouse) [new]
1 
P56962 STX17
STX17_HUMAN
171 180 QNAAESWETLEADLIELSQL TP 5 Homo sapiens (Human) [new]
2 
P49023 PXN
PAXI_HUMAN
39 48 PTGNHTYQEIAVPPPVPPPP TP 4 Homo sapiens (Human) [new]
1 
P46934-4 NEDD4
NEDD4_HUMAN
264 274 RESSENWEIIREDEATMYSN TP 5 Homo sapiens (Human) [new]
1 
P35193 ATG19
ATG19_YEAST
411 415 SISLSYDGDDNEKALTWEEL TP 3 Saccharomyces cerevisiae S288c [new]
2 
P27797 CALR
CALR_HUMAN
199 208 GSLEDDWDFLPPKKIKDPDA FP 4 Homo sapiens (Human) [new]
P17302 GJA1
CXA1_HUMAN
3 11 MGDWSALGKLLDKVQAYSTA FP 4 Homo sapiens (Human) [new]
2 
P06821 M
M2_I34A1
88 96 KEQQSAVDADDGHFVSIELE TP 5 Influenza A virus (A/Puerto Rico/8/1934(H1N1)) [new]
O95197 RTN3
RTN3_HUMAN
246 256 DSPESPFEVIIDKAAFDKEF TP 4 Homo sapiens (Human) [new]
5 
P0CK59 BALF1
BALF1_EBVG
144 153 YNDHYDYWSRLRVVLCYTVV FP 2 Human herpesvirus 4 (Epstein-Barr virus) [new]
O70511 Ank3
ANK3_RAT
1988 1997 HSPEDDWTEFSSEEIREARQ TP 3 Rattus norvegicus (Norway rat) [new]
2 
O35129 Phb2
PHB2_MOUSE
119 128 AQELPSMYQRLGLDYEERVL FP 3 Mus musculus (House mouse) [new]
O60238 BNIP3L
BNI3L_HUMAN
35 41 PAGLNSSWVELPMNSSNGND TP 6 Homo sapiens (Human) [new]
1 
D0NBE6 PexRD54
RD54_PHYIT
377 381 AEALQFFRKAKPLDFDWEIV TP 10 Phytophthora infestans T30-4 [new]
1 
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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