The Eukaryotic Linear Motif resource for
Functional Sites in Proteins

ELM candidate motifs

ELM annotation process is a tedious and time-consuming process involving critical reading of primary and secondary literature, finding motif instances, generating multiple sequence alignments and more. In order not to loose track of possible annotations, we keep the following list of candidate motifs.
We invite researchers to send us their feedback and expert opinion on these classes and to contribute novel motif classes that will be added to the candidate page and ultimately be turned into full ELM classes. Minimum requirements are at least one literature reference as well as a short description. In addition, a draft regular expression or a 3D structure showing the relevant interaction would also be helpful.

Currently 335 candidates need annotation: (Add a new candidate)

Detailed Status:
first draft: 224
undergoing annotation: 17
fully annotated: 79
not annotatable: 2
deleted: 12
annotatable: 1
Identifier Model References Description Notes Status
MOD_ARK/PRK/AAK1_1 [LI]..Q.(T)G 12956961,
9885245,
11739778,
13679512,
Ricotta,2002
Optimal phosphorylation site motif for mammalian AAK1 and yeast PRK/ARK kinases that are involved in the regulation of endocytosis. A more relaxed version of the motif is [L/I/V/M]xx[Q/N/T/S]xTG first draft
[Edit]
[Delete]
LIG_APP_AP2beta_1 [FL]..G[FL].DF Schmid,2006, 1E42
Motif binding to the side site of the C-terminal beta2-appendage domain of the large subunit beta2-adaptin. This interaction is part of the system for recruiting partners for assembly of clathrin-coated vesicles. first draft
[Edit]
[Delete]
Lig_MHD_deltaCOP_1 W.{1,6}[WF] 26578768, 5FJZ
The delta-COP subunit of the Coatomer complex binds a Wx(1-6)[WF] motif in interacting proteins like Dsl1 tether (yeast) and ArfGAP1 (mammal). The motif binds to the mu homology domain of delta-COP first draft
[Edit]
[Delete]
LIG_MHD_FCHO_1 DPFxxxDPFxxDPF 27237791
25061211
The motif binds to mu humology domain (MHD) of FCHO with an affinity of 2μm. first draft
[Edit]
[Delete]
MOD_LOK [KR]Y.[ST] 16616188 LOK kinase optimal phosphorylation site. LOK is a basophilic kinase with unusual Y preference at position 2. first draft
[Edit]
[Delete]
eIF2alpha_binding_motif Rx[Gnl]x1-2Wxxx[Arlv]x[Dn][Rg]xRFxx[Rlvk][Ivc] 26100893
The eIF2α-binding motif is characterized by the consensus sequence Rx[Gnl]x1-2Wxxx[Arlv]x[Dn][Rg]xRFxx[Rlvk][Ivc], where capital letters are preferred and x is any residue. This eIF2α-binding motif is found in the PP1 regulatory subunits GADD34, CReP, and several viral proteins including, ICP34.5, DP71L, and CNPV231. first draft
[Edit]
[Delete]
LIG_PEX19_mPTS_1 15133130 PEX19 is thought to be the receptor for importing peroxisomal membrane proteins by binding to a short mostly hydrophobic peptide, the mPTS. first draft
[Edit]
[Delete]
LIG_AIR1_Trf4 IWRxY 21878619, 22402490, 3NYB The Air1-Trf4 interaction motif is important for TRAMP formation, which plays a major role in RNA surveillance and polyadenylation of RNA targets, marking them for exosomal degradation. The motif was found in yeast and presumably is conserved in an human orthologue of Air1. Motif in linker region between zinc knuckle 4 and 5 of Air1. first draft
[Edit]
[Delete]
TRG_Transportin_M9nls_1 R..PY..P 7730395,
15703190,
16901787,
22778397,
16179349,
4FDD,
4JLQ,
2OT8,
2Z5K,
2Z5O,
2Z5N
Non-canonical NLS bound by transportin/karyopherin beta. Found in some RNA processing proteins, in T-box and ATF4/5 transcription factors. Always has a PY doublet, usually preceded by positively charged residues and also a weakly conserved second hydrophobic motif. Mutations in M9 class NLSes cause Di George syndrome (mutated in Tbx1) and ALS (mutated in FUS, EWS, TAF15). Observed instances are quite variable and likely require several motif patterns to capture the range of possibilities. first draft
[Edit]
[Delete]
Lig_IntegrinA4B1_MLD MLD 14769041 Extracellular alpha4beta1, alpha9beta1 and alpha7beta4 Integrin-binding motif. Motif was first identified in snake venom disintegrins. Not sure if a native protein with MLD has been identified. first draft
[Edit]
[Delete]
LIG_RGD_High RGDL..[LI] 25383667
4UM8
4UM9
Integrin alphaVbeta6 binds with high affinity to a RGDLXXL/I motif within the prodomains of ​TGF-β1 and ​TGF-β3. first draft
[Edit]
[Delete]
LIG_integrinA1B1_KTS [RK]TS 18774946, 21148411, 22778902 Extracellular alpha1 beta1 Integrin-binding motif. Motif was first identified in snake venom disintegrins. Also found in secreted proteins of some blood-sucking invertebrates. These integrins are collagen-binding and have a role in angiogenesis. Possible cellular KTS motif found in mouse/human ADAM-9. first draft
[Edit]
[Delete]
DOC_PP2B_PxIxI_2 .P.LP[IL]. 12601010 A calcineurin-binding motif in viral protein p12 from HTLV; competes with NFAT for binding to calcineurin. The instance does not match the regular expression of our DOC_PP2B_PxIxI_1 entry (.P[^P]I[^P][IV][^P]) as it contains a leucine in the invariant isoleucine position and a proline in the next [^P] position; paper should be checked and if correct the RE should be revised or a second variant should be created. first draft
[Edit]
[Delete]
LIG_MSL3 AFG..[LIV]..[LIMF].{4,10}F.LPW 21217699, 2Y0N Long extended peptide wrapping around the MRG domain of MSL3, with one part forming a short hairpin; highly conserved hydrophobic residues (mainly Phe) insert into different hydrophobic pockets on the MSL3 surface; found in MSL1 (subunit of the male-specific lethal complex involved in gene dosage compensation); (see also literature on WDR5-binding motifs in ELM). 21217699 discusses other proteins using similar surfaces/sequences for binding, see references therein; model presented here only describes core, should be extended at the N-terminus first draft
[Edit]
[Delete]
LIG_MOF E.[LI].D[^P][^P][FY][^P][^P][^P]H[^P][KR] 21217699, 2Y0M Helical motif that binds the HAT domain of the histone acetyltransferase MOF; found in MSL1 (subunit of the male-specific lethal complex involved in gene dosage compensation) and NSL1 (subunit of the nonspecific lethal complex involved in transcription regulation and cell reprogramming) (see also literature on WDR5-binding motifs in ELM). first draft
[Edit]
[Delete]
LIG_NRBOX_AR_2 F..LF 15178743 LBD-binding motif in the N-terminal region of androgen receptor that binds to coactivator-binding groove on androgen receptor (AR), competing with coactivators. This groove is deeper on AR compared to for instance estrogen receptor, which does not bind this motif. first draft
[Edit]
[Delete]
LIG_Munc18/Sec1 D[RL].{3,4}[FL] 23572542,20884800,21139055,11879635,12426383,1MQS Conserved Munc18/Sec1-binding peptide present in N-terminal region of eukaryotic SNARE proteins, e.g. vertebrate syntaxin 5, yeast Sed5 and Ufe1, and arabidopsis SYP121. first draft
[Edit]
[Delete]
LIG_KC1 F.RF 20884800,23572542 Motif in arabidopsis SNARE protein SYP121 required for binding to K+ channel subunit KC1; overlaps with a Sec1/Munc18-binding motif. first draft
[Edit]
[Delete]
LIG_AP_GAE_2 W..[FW] 14973137,17506864,2DWX Motif in hinge region of GGA1, also in NECAP1 and amphiphysin II, that mediates interaction with the AP-1 gamma-ear domain; binds to same or overlapping site as LIG_AP_GAE_1 first draft
[Edit]
[Delete]
LIG_OST ([FVL].C)|(C.[FVL]) 24685145,4M91,4M92 peptide that binds to the N33/Tusc3 (and maybe paralogous IAP/MagT1) subunit of the oligosaccharyl transferase (OST) complex to improve glycosylation efficiency; found in OST substrates; peptides can be accommodated in opposite orientations; peptide is covalently anchored to N33/Tusc3 via the cysteine residue (disulfide link); prefers Leu, Val or Phe in the -/+2 position relative to Cys; also backbone interactions first draft
[Edit]
[Delete]
LIG_CagA 24474782, 4IRV N-terminal domain of the Cytotoxin Associated Gene A (CagA) of Helicobacter pylori binds to a 20aa long helical motif in the Apoptosis-stimulation protein p53-2 (ASPP2). first draft
[Edit]
[Delete]
LIG_WIRS [FMYL].[TS]F.. 4N78
24439377
24439376
Motif binds to a conserved WAVE regulatory complex surface formed by Sra and Abi subunits. Motif therefore directly links diverse membrane proteins to the WRC and actin cytoskeleton first draft
[Edit]
[Delete]
MOD_N-GLC_2 [DE].(N)[^P][ST].. 16619027
21209858
20523900
20847188
20581208
similar regular expression to MOD_N-GLC_1 but also found within bacteria and archea. bacterial N-glycosyltransferases exhibit a more stringent specificity for the acceptor site than the eukaryotic counterpart. This restricts glycosylation to a narrow set of polypeptides first draft
[Edit]
[Delete]
CLV_MetAP1 ^M[ACGPS][^P]... Xiao,2010, 12665801, 18828628, 10574784, 16274222, 12475202 Target site for cleavage of N-terminal methionine by methionine aminopeptidase MetAP1. Overlapping substrate specificity with MetAP2 but MetAP1 cannot accommodate the larger side chains tolerated by MetAP2 (Thr and Val) in the P1' position due to its smaller active site. Disfavors acidic residues in positions P2' to P5'. His and Trp were underrepresented in P2' and P3' in the most active substrate peptides as determined by peptide library screening. Strong preference for Ala in P1'. first draft
[Edit]
[Delete]
CLV_MetAP2 ^M[ACGPSTV][^P]... Xiao,2010, 12665801, 18828628, 10574784, 16274222, 12475202 Target site for cleavage of N-terminal methionine by methionine aminopeptidase MetAP2. Overlapping substrate specificity with MetAP1 but can accommodate larger side chains of Thr and Val in the P1' position due to its larger active site. Disfavors acidic residues in positions P2' to P5'. Disfavors Trp at P2' and P3'. first draft
[Edit]
[Delete]
MOD_NatF ^(M)[LFIWK]... 21750686, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatF/NAA60. See 19660095 for nomenclature. Found only in higher eukaryotes, consequently MK termini are rarely found to be acetylated in yeast. first draft
[Edit]
[Delete]
MOD_NatE ^(M)[KLMA]... 3TFY, 21900231, 21383206, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatE/NAA50. See 19660095 for nomenclature. Specificity partially overlaps with NatB and NatC. first draft
[Edit]
[Delete]
MOD_NatD 19332560, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site in histones H2A and H4 for N-terminal acetylation (SGRGK termini) by NatD/NAA40 after cleavage of initiator methionine. See 19660095 for nomenclature. In vivo substrate specificity for NatD is determined by N-terminal 30-50 amino acid region in its histone substrates, instead of the first few residues (2-5) in case of the other N-acetyltransferases. first draft
[Edit]
[Delete]
MOD_NatC ^(M)[LFIW]... 23613772, 10545125, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatC/NAA30. See 19660095 for nomenclature. Might also accept a Tyr residue in the second position. Specificity partially overlaps with NatB and NatE. first draft
[Edit]
[Delete]
MOD_NatB ^(M)[DENQ]... 22814378, 12507466, 10545125, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatB/NAA20. See 19660095 for nomenclature. Specificity partially overlaps with NatC and NatE. first draft
[Edit]
[Delete]
MOD_NatA ^([SATVCG])[^P]... 4KVM, 19420222, 10545125, 21383206, 23912279, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for N-terminal acetylation by NatA/NAA10 after cleavage of initiator methionine. See 19660095 for nomenclature. There might be subtle differences in specificity between yeast and human. NatA might also target N-terminal acidic residues, likely only in higher eukaryots and when acting independently from its auxiliary protein NAA15. first draft
[Edit]
[Delete]
LIG_Talin [WY].{4}NP.Y 15362227, 20332112, 19903453, 19863457 Composite motif in the C-termal region of integrin. It is regulated by tyrosine phosphorylation and PTB domain binding at NPxY. Unphosphorylated form binds talin by beta addition. first draft
[Edit]
[Delete]
LIG_FDF FDF|.DW 19285948, 2WAX, 2WAY, 23851565, 4BRU, 4BRW Motif in regulators of mRNA decapping like Pat1 and Edc3; mediates binding to the RecA2/Helicase_C (PF00271/IPR001650) domain of yeast Dhh1 and human Ddx6 RNA helicases. Edc3 contains the FDF variant, as well as yeast Pat1, while vertebrate Pat1 has the DW variant. Interactions mediated by this motif likely regulates binding of RNA to the helicase. In Edc3 the motif has been described as part of the FDF domain (PF09532/IPR025762), an alpha-helical domain with the conserved FDF sequence at the N-terminal. Structures show that additional binding elements determine the interactions. A helical acidic motif N-terminal to the FDF/DW motif in Pat1 binds to a second pocket on Dhh1, while a helical segment (F[DN]K) located C-terminal of the FDf motif in Edc3 binds yet another pocket on Ddx6/Dhh1. first draft
[Edit]
[Delete]
FUN_FG_nucleoporin (FG)n 18688269, 12065398, 12372823, 17161424, 16338415 Motif present in nucleoporins that function as intramolecular cohesion elements imparting order to the FG domain and compacting its ensemble of structures into native premolten globular configurations. first draft
[Edit]
[Delete]
LIG_Kln1_MELT_1 ..M[ED][LIVMF]T.. 24066227,
24361068,
4bl0
Repeated semi-conserved motifs with the consensus MELT are found in Kln1/Spc105 and bind to the BUB3 beta-propeller as part of the spindle assembly checkpoint. The motifs are phosphorylated on the Thr residue by Mps1. A structure of the motif in complex with the Bub3 domain has been solved in the yeast system. By sequence alignment, the mammalian MELT repeats might be longer than the yeast ones. The core MELT should be similar though. Backbone interactions extend beyond the core MELT motif: Pro might be excluded from some adjacent positions. first draft
[Edit]
[Delete]
LIG_CYCLIN_2 L..P[ILVMF].[ILVMF] or LLPP 21945277, 21658602, Koivomagi,2013 These non-canonical cyclin boxes bind preferentially to the yeast cyclin Cln2 and enhance phosphorylation of Cdk substrates in a cyclin-specific manner. found in yeast. first draft
[Edit]
[Delete]
Lig_CaM_1-5-10 ...[FILVW]...[FILVW]....[FILVW] Rhoads,1997 Several helical motif variants can bind calmodulin, including the Ca++ independent IQ motif and the 1-8-15 and the 1-5-10 motifs. The 1-5-10 motif is defined by the hydrophobic residue spacing. Other key features are lack of proline and a preference for positive and against negative charge. Additional info here

http://calcium.uhnres.utoronto.ca/ctdb/ctdb/

http://structbio.vanderbilt.edu/cabp_database/index.html
first draft
[Edit]
[Delete]
Lig_CaM_1-8-15 [FILVW]......[FILVW].....[FILVW] Rhoads,1997 Several helical motif variants can bind calmodulin, including the Ca++ independent IQ motif and the 1-8-15 and the 1-5-10 motifs. The 1-8-15 motif is defined by the hydrophobic residue spacing. Other key features are lack of proline and a preference for positive and against negative charge. Additional info here

http://calcium.uhnres.utoronto.ca/ctdb/ctdb/

http://structbio.vanderbilt.edu/cabp_database/index.html
first draft
[Edit]
[Delete]
LIG_Sliding_Clamp QL.L.[FL] 14729336 first draft
[Edit]
[Delete]
LIG_SCF-TrCP1_2 [EDST][ESTD][GAS].{1,3}[STD] 19150432
14676825
15070733
15845771
18354483
17387146
18378670
15917222
15767683
Zhao,2010
20858893
23948254
non-canonical variants of the LIG_SCF-TrCP1_1 first draft
[Edit]
[Delete]
LIG_Menin_MBM_2 20961854,
22327296
Bipartite interaction interface recognised by Menin. MBM1 (90nM) and MBM2 (1,400 nM) bind with different affinities but together bind with a much stronger affinity (6.8 nM). Exact residues are unknown but fall between residues 23-40. This entry may be fused with MBM_1 in light of the crystal structures of JunD and MLL1 complexes first draft
[Edit]
[Delete]
LIG_Menin_MBM_1 ...R{0,2)FP[GA].P 20961854,
22327296,
3U85,
3U86
Part of Bipartite interaction interface recognised by Menin. MBM1 (90nM) and MBM2 (1,400 nM) bind with different affinities but together bind with a much stronger affinity (6.8 nM). MBM1 binds in an extended conformation. Crystal structures with MLL1 and JunD define this core part Positive charged residues c-terminally are also critical for the motif and if possible should be added to the core motif. first draft
[Edit]
[Delete]
MOD_Citrullination ^M{0,1}[SGAT].R. 16567635
23818587
Peptidylarginine deiminase 4 (PAD4) is a Ca2+-dependent enzyme that converts arginine and methylarginine residues to citrulline. Originally identified in Histones, more recently PAD4-mediated citrullination of GSK3β has been discovered may not be only N-terminal first draft
[Edit]
[Delete]
MOD_PKB_1 R.R[^PRK].[ST][FY^P] Yang,2002, 1O6L Improved P-site motif for PKB. Position -2 cannot allow Pro due to backbone H-bond. Position -2 considered not to allow R on structural grounds: this would differentiate relative to some other basophilic kinases. Position -2 has a strong T preference too. Position +1 is probably not strong enough to demand hydrophobic residue, though clearly favouring one. GSK3beta p-site is close to optimal. first draft
[Edit]
[Delete]
Mod_PIMK_1 R.R[RKH^PDE].[ST][G^P] 16227208,2BZK PIM kinases of the CAMK-related group are mediators of cytokine signaling pathways in hematopoietic cells. Their P-sites are basophilic with a preference for R at the -5 and -3 positions like some other basophilic kinases. They have a weaker preference for positive charge at -2 (and cannot tolerate P). A weak G preference is found at +1 and P is rejected. first draft
[Edit]
[Delete]
MOD_LRRK2_1 [FY].(T).R 21060682 The Parkinson's kinase LRRK2 phosphosite motif derived by oriented peptide library. Y is weaker than F at -3. K and R are generally favoured in the +1,+2,+3 positions of the motif. first draft
[Edit]
[Delete]
LIG_Neur_NXXN N..N..L 19580805 N-rich motifs such as N..N..L in bearded and QN..NA in Delta reported to bind to the Neuralized E3 ligase. Motifs seem to play a role in both inhibition and activation of Notch signalling.

first draft
[Edit]
[Delete]
LIG_PSI_ProlineMotif_1 P.PPP 15990112 Proline-rich sequence binding to small double alpha-helical module known as PSI A,B box or PFAM DUF1897 found as two or three copies in a few RNA-binding proteins e.g. PSI, KHRP. Aromatic residues on one helical face make hydrophobic interactions with Pro residues in the peptide motif which is found in U1-70k protein of the U1 snRNP. In fly, involved in P-element transposase alternative splicing. Strong phylogenetic conservation suggests that there is a more general cellular function. Not clear if this interaction is well enough described yet to make a motif pattern capturing the allowed Pro residue spacing and any possible additional residues. first draft
[Edit]
[Delete]
TRG_NoDS RR[IL].{1,10}[ILVF][ILVF][ILVF] 22284675 Nucleolus targeting signals that results in sequestration of proteins by ncRNA first draft
[Edit]
[Delete]
MOD_SUMO_SCM [PG].{0,4}[VILMAFP](K).E.{0,3}[PG] 10913186, 22829593, 12429819, 20150575 Synergy Control Motif (SCM) found in steroid receptors such as Androgen Receptor, Glucocorticoid Receptor transcription factors. SCM consists of a core 4 residue sumoylation site and within 3-4 residues N or C terminal of this site, a Pro or Gly residue is found. Mutations in these Pro or Gly residues are reported in various diseases including prostate and testicular cancer. first draft
[Edit]
[Delete]
LIG_UBAN DF..ER 19185524, 18212736, 20428114 di-ubiquitin recognition motif found in ABIN proteins, Optineurin, and NEMO. The motif is required for inhibition of NFkB activation. Missense mutations disrupting the motif have been shown to be causal in diseases including Diffuse Large B-Cell Lymphoma and Amyothrophic Lateral Sclerosis. first draft
[Edit]
[Delete]
LIG_JAK_Box1 P.[IV]P.P[EK] 12374810,
7896787
Box1 motif conserved in the common gamma subunit of cytokine receptors including erithropoietin receptor, interleukin3/5/6 receptors, prolactin receptor, interferon-gammaR receptor, and growth hormone receptors. The motif is required for association with JAK kinases. first draft
[Edit]
[Delete]
LIG_sHSP_IxI_1 .I.[IV]. 23188086,
23340341
Oligomerisation motif of alpha-crystallins and related small heat shock proteins. first draft
[Edit]
[Delete]
LIG_SH3_8 [RK]..[RK] 12176364
1H3H
Kojima,2004
non canonical SH3 binding motif confers specificity for the interaction between Gads and SLP-76 in T cell signaling.
12176364 analyses the binding using short peptides. SLP-76 contains two R..K motifs, but only the first (PSIDRSTK) binds, the second (TFPSRSTK) does not (or wasn't done)
first draft
[Edit]
[Delete]
MOD_Spalmitoyl_3 (C)CIF 19092927 variant motif; instance does not match current RegEx instance in switches.elm: SWTI000549 CDC42_HUMAN (P60953-1) 188 191 first draft
[Edit]
[Delete]
MOD_CDK_3 ([ST])P... Byeon,2005 variant motif; instance does not match current RegEx instance in switches.elm: SWTI000284 MK67I_HUMAN (Q9BYG3) 235 241 first draft
[Edit]
[Delete]
LIG_14-3-3_4 [RHK][STALV].([ST]).[PESRDIFTQL] 17166838 Slightly modifified LIG_14-3-3_3 motif, allowing for Leucine in last position to match instance. instance in switches.elm: SWTI000583 HAP1_RAT (P54256-2) 594 598 first draft
[Edit]
[Delete]
LIG_Dynein_DLC8_2 [KR].TMT 17029413;16981716 variant instance in switches.elm: SWTI000541
MYO5A_HUMAN (Q9Y4I1) 1286 1290
first draft
[Edit]
[Delete]
CLV_CASPASE3_1 D..D 12637508 relaxed Caspase3-1 cleavage site instance in switches.elm: SWTI000550 CEAM1_MOUSE (P31809) 457 460 first draft
[Edit]
[Delete]
LIG_S100A4_1 22460785,22483112,3ZWH,2LNK Ca2+ dependent binding of myosin IIA peptide to S100A4 dimer, involved in filament disassembly. The peptide binds across the S100A4 dimer surface (1:2 stoichiometry). Hydrophobic side chains insert into hydrophobic pockets on the dimer. In addition, charged and polar peptide residues form hydrogen bonds and salt bridges with complementary S100A4 residues. Composite binding site, will be added to switches.ELM. first draft
[Edit]
[Delete]
LIG_S100A10_AnxA2_1 .[^FLVIMAWP][GLVAI][^FLVIMAWP][FIL][PVA][KHR][MIFLV][KHR].[GP][KR][FILV][^FLVIMAWP] 21949189, 23275167, 4DRW,4FTG Several regions in C-terminal of membrane-repair protein AHNAK bind to AnnexinA2-S100A10 (2:2) heterotetramer often localised at plasma membrane. A single AHNAK peptide binds across the tetramer surface, making contacts with all 4 components of the S100A10-AnxA2 complex. Binding mainly governed by hydrophobic interactions between AHNAK side chains and pockets on S100A10 (some with additional residues of AnxA2) and hydrogen bonds with backbone atoms of AHNAK. Composite binding site, will be added to switches.ELM. first draft
[Edit]
[Delete]
TRG_NES Mazanka,2008 NES first draft
[Edit]
[Delete]
LIG_BROMO_BET (K)[GILVMF]{0,1}[^MFYLW].(K) 2WP2
19794495
22464331
Diacetylation recgnition motif for bromodomain of BET family first BRDs of the BET family first draft
[Edit]
[Delete]
LIG_BROMO 20502673,11080160 1E6I The Bromodomain binds acetylated lysine residues in the flexible N- and C-terminal tails of histones. first draft
[Edit]
[Delete]
TRG_NLS Shin,2002 1594241 Duprez,1999 21092142 21182795 non-canonical nuclear localisation signals first draft
[Edit]
[Delete]
MOD_EZH2 RKS 23063525 EZH2 can monomethylate the lysine on a RKS histone-like sequence on RORα leading to its subsequent ubiquitination through the chromo domain of DCAF1 see LIG_CHROMO for DCAF1 recognition motif first draft
[Edit]
[Delete]
Mod_PLK_1 (.[DEN][^GP]([ST])[FILMVW]..) or (.[DEN][^GP]([ST])[^P][FILMVW].) Alexander,2011
Revised PLK1 phosphosite based on peptide data. Better description than the current ELM model. first draft
[Edit]
[Delete]
LIG_MBT 20502673 1OYX 12842041 Malignant brain tumor (MBT) repeats have been implicated as methyl-lysine binding modules. first draft
[Edit]
[Delete]
LIG_CHROMO ARK[ST] 20502673 1KNA 11859155 Chromo domains promote binding to methylated lysines in Histone H3 tails. first draft
[Edit]
[Delete]
MOD_SUMO_PHOS [VILMAFP](K).[ST]. Picard,2012 Novel Sumoylation site found in Estrogen receptor beta connected to a GSK-beta phosphorylation site first draft
[Edit]
[Delete]
LIG_KIX_CBP [DEST][LMYI]..[LIF][LIV] 22474372, 2KWF, 16253272, 2AGH, 9413984, 1KDX, 19220000, 17467953 hydrophobic motif found in transcription factors (FOXO3a, CREB, c-Myb, p53, TCF4...) that interacts with the KIX domain of CBP/p300 to recruit this transcription coactivator. Promiscuous as they might also bind to TAZ1 and TAZ2 domains of CBP/p300. For FOXO3a, phosphorylation of overlapping serine increases affinity. first draft
[Edit]
[Delete]
LIG_MO25alpha_WEF_1 WEF 14730349, 19892943, 1UPK The WEF motif contributes to docking the STRADalpha pseudokinase to MOF25alpha in the LKB1-STRAD-MO25 complex System of increasing interest as LKB1 (STE11) is a tumour suppressor kinase and has recently been is associated with primary cilia and WNT/HH signalling
first draft
[Edit]
[Delete]
LIG_SH2_IA (Y)[DE][DE][AFILVWY] 17956856 Subgroup IA, which consists of members of the SRC, SYK/ZAP-70, and TEC kinase families as well as the adaptor proteins NCK1 and NCK2, selects for the common motif (Y)[DE][DE][AFILVWY] first draft
[Edit]
[Delete]
LIG_SH2_III (Y)..Q 17956856 Group III comprises the STAT family of SH2 domains.
first draft
[Edit]
[Delete]
LIG_SH2_IID (Y)... 17956856 this is the generic motif for Group 2 SH2 domains. first draft
[Edit]
[Delete]
LIG_SH2_IIC (Y)... 17956856 this is the generic motif for Group 2 SH2 domains. first draft
[Edit]
[Delete]
LIG_SH2_IIB (Y)[ED].[AFILVWY] 17956856 Subgroup IIB selects for a hydrophobic residue at P+3 within the general consensus (Y)[ED].[AFILVWY]. The SHC and SHB families of adaptor proteins, BLNK, and SLNK all belong to this subgroup
first draft
[Edit]
[Delete]
LIG_SH2_IIA (Y)[AFILVWY].[AFILVWY] 17956856 Subgroup IIA loosely selects for the degenerated motif (Y)[AFILVWY].[AFILVWY]. This subgroup is represented by the SH2 domains from several protein families that include VAV, phosphatidylinositol 3-kinase, PLCG1, PTPN, and SOCS.
first draft
[Edit]
[Delete]
LIG_SH2_IE (Y)[DEKNPR][DEKNPR][AFILVWY] 17956856 this is the generic motif for Group 1 SH2 domains. first draft
[Edit]
[Delete]
LIG_SH2_ID (Y)[DEKNPR][DEKNPR][AFILVWY] 17956856 this is the generic motif for Group 1 SH2 domains. first draft
[Edit]
[Delete]
LIG_SH2_IC (Y).R 17956856 Subgroup IC,
identifiable by a strong proclivity for an Asn residue at P+2,
forms the second largest subgroup within group I with 18
members. It includes not only the GRB2/GRAP/GADS family
but also the GRB7/10/14 family, the tensin family, and the
Fes/Fer family.
first draft
[Edit]
[Delete]
LIG_SH2_IB (Y)..[AFILVWY] 17956856 Subgroup IB, including SH2 domains from
SH2D1A, SHIP1/2, and CRK/CRKL, are
related to one another by a shared propensity for a hydropho-
bic residue at P+3. Selectivity at P+1 or P+2 for this group
of SH2 domains is wider than for subgroup IA
first draft
[Edit]
[Delete]
TRG_AP2beta_CARGO_2 [FY]F.{6}W.[FY] 19287005 non-canonical AP2-beta2 binding found in isoform of PIPKIγ first draft
[Edit]
[Delete]
TRG_NES_CRM1_2 L.{2,3}L.L 11074002 very general NES first draft
[Edit]
[Delete]
LIG_PTB_Talin SPLH 1Y19, 2G35
12422219
Non-canonical PTB binding motif found to bind to the Talin PTB domain motif only found in PIP5K1C for far. Waiting for more instances before annotation first draft
[Edit]
[Delete]
CLV_C14_Metacaspase 17028019,
18005666,
Sundstrom,2009,
21597462
Metacaspases are distantly related to caspases and are found in protozoa, fungi and plants. They are involved in regulation of different cell biological processes, like programmed cell death and development. Contrary to caspases which cleave specific after aspartate, metacaspases cleave specific after arginine and lysine. Depending on their prodomain metacaspases were distinguished into type I and II. Less is known about metacaspases' cleavage motif.
Only 3 metacaspases' substrates were described.

first draft
[Edit]
[Delete]
TRG_LysEnd_APsAcLL_2 [DERQ].{2,4}L[LVI] 18315530
Kirchhausen,1999
Slight variation of TRG_LysEnd_APsAcLL_1 first draft
[Edit]
[Delete]
TRG_MLS 22178138
10837244
16616497
The N-terminal Mitochondrial localisation signal recognised by Tom70. Could not define regular expression first draft
[Edit]
[Delete]
LIG_IQ_3 [FILV]Q...[RK]G...[RK]..[FILVWYM] Rhoads,1997
8805510
8127365
12351846
Bahler,2002
extended IQ motif first draft
[Edit]
[Delete]
LIG_IQ_2 [FILV]Q...[RK] Rhoads,1997
8805510
8127365
12351846
Bahler,2002
IQ-like motif. first draft
[Edit]
[Delete]
LIG_PCNA_2 [ILVM][^ILVM][DHFM][ILVM] 11682605 slight variation on original PCNA motif first draft
[Edit]
[Delete]
LIG_BIR_internal A.[AP]. 14523016 Internal BIR-binding site. In this case, precursor mitochondrial localisation signal is removed exposing BIR site first draft
[Edit]
[Delete]
LIG_PI(4,5)P2 [KR].{3,4}K.[KR][KR] 9891784,Kojima,2004 lipid binding motif for PI(4,5)P2 first draft
[Edit]
[Delete]
LIG_Filamin_2 Y..A[VIL]...[VIL] 16455489
2BRQ
Based on integrin binding to filamin
No mention of importance of threonines defined in LIG_Filamin
first draft
[Edit]
[Delete]
LIG_TPR_4 [ST].[ST] 21454478
3Q4A
phosphorylated version of LIG_TPR found in Smad 1/5 first draft
[Edit]
[Delete]
LIG_TPR_3 K[IL].{0,2}Q 18759457
17942943
internal TPR binding motif with similatities found in androgen receptor and vpu unsure of veracity first draft
[Edit]
[Delete]
TRG_multiple 19482617 Review of several motifs responsible for internalization and trafficking
of cell-surface membrane receptors
NP.Y is mentioned in LIG_PTB_Phospho_1 first draft
[Edit]
[Delete]
LIG_MIU [DE][LIVY].[LIV]A..[LIVY]..[DE]{DE] 16499958
2C7N
2C7M
19217402
MIU (motif interacting with ubiquitin; also known as IUIM or inverted UIM) first draft
[Edit]
[Delete]
LIG_TAZ2 F.[DE]...L 10196247,19217391,16319895, 2KJE, 2K8F Binding motif for the TAZ2 domain in transcriptional adapter protein CBP/PCAF/p300 First attempt to annotate failed. Needs more information. A better structure for the P53 instance would be useful. first draft
[Edit]
[Delete]
LIG_DUIM [DE].[LIVY]..A[LIVYM]A.S.[SA][DE] 16462748 2D3G double sided ubiquitin interacting motif first draft
[Edit]
[Delete]
LIG_UIM [DE][DE]..[ILVY]..A[ILVY].S.. 16462748 12970172 1Q0V 2D3G 12750381 1O06 Ubiquitin interacting motif first draft
[Edit]
[Delete]
MOD_N-GLC_3 NG. 20510933 21978957 Non-canonical N-glycosylations sites found in the mouse glycoproteome first draft
[Edit]
[Delete]
MOD_N-GLC_4 N.V 20510933 21978957 Non-canonical N-glycosylations sites found in the mouse glycoproteome first draft
[Edit]
[Delete]
LIG_PCNA_PIP_2 ...[LIM][DE].[FHY][FHY]. 19208623, 2ZVM,Kim,2010,Shibutani,2008 Non-canonical PIP box, missing the p1 glutamine. Mediates binding to PCNA. Found in Polη, Polκ. The PIP boxes of Xic1 in X. laevis and E2F in D. melanogaster overlap the PIP degron LIG_CRL4_Cdt2_1 and LIG_CRL4_Cdt2_2, respectively. first draft
[Edit]
[Delete]
CLV_C14_Caspase-1 [WFYML][^P].D 1221285 1236692 15296730 Caspase-1 is involved in inflammation. Motif suggestion is based on in vitro data. Optimal described sequence is WEHD. For protein substrate see MEROPS or CutDB first draft
[Edit]
[Delete]
LIG_WW_Nedd4L .(S)P.L(S)PN Aragon,2011, 2LAJ Motif in Smad3 that binds to the third WW domain of Nedd4L. Phosphorylation of Smad3 by CDK8/9 and GSK3 recruits ubiquitin ligase Nedd4-like via its third WW domain; second WW domain displaces Pin1 at WW motif upstream; leads to Smad3 destruction. first draft
[Edit]
[Delete]
MOD_Geranyl_CAAXbox_1 (C).[LIVM][ILMV]$ 12702202 Motif modified by Geranylgeranyltransferase I (GGT1). Should replace current MOD_CAAXbox to define specificity. first draft
[Edit]
[Delete]
MOD_Farnesyl_CAAXbox_1 (C).[LIVM].$ 12702202 Motif modified by Farnesyltransferase. Should replace current MOD_CAAXbox to define specificity. first draft
[Edit]
[Delete]
LIG_DCUN1_1 (M)[IL].L Scott,2011 3TDZ Acetylated N-terminal methionine motif that mediates binding to the DCUN domain of E3 ligase DCN1 found in E2 ligase Ubc12. first draft
[Edit]
[Delete]
LIG_LCK_1 C.CP 14500983 1Q69 1Q68 Found in CD4 and CD8. Beautiful mechanism where LCK contributes 2 cysteines and CD4/CD8 contribute 2 cysteines to bind zinc and form a "zinc clasp" binding site. 400nM affinity. Also buries a di-leucine sorting signal regulating trafficking. May not be a short linear motif by some definitions. first draft
[Edit]
[Delete]
LIG_TKB (Y)[TS]..PT 20877636, 18273061, 3OB1, 3OB2 Recognition motif in EGFR and Sprouty2 for non-canonical SH2 domain (TKB domain) in E3 ubiquitin ligase c-Cbl first draft
[Edit]
[Delete]
CLV_C14_Caspase4-5 [LIVMWYF][EDQ][^RKGL]D 1221285 1236692 Caspase-4 and -5 are involved in inflammation. Motif suggestion is based on in vitro data. Optimal described sequence is [WL]EHD. For protein substrate see MEROPS or CutDB first draft
[Edit]
[Delete]
CLV_C14_Caspase-2 [DEIL].[DEFY]D 1221285 1236692 12920126 Caspase-2 induces the intrinsic apoptotic pathway during cell stress signaling. Motif suggestion is based on in vitro data. Optimal described sequence is DEHD. For protein substrate see MEROPS or CutDB first draft
[Edit]
[Delete]
CLV_C14_Caspase-9 [^RK][EDQ]HD 1221285 1236692 11734640 Caspase-9 is an initiator caspase in the intrinsic apoptotic pathway and cleaves executor caspases. Motif suggestion is based on in vitro data. Optimal described sequence is LEHD. For protein substrate see MEROPS or CutDB first draft
[Edit]
[Delete]
CLV_C14_Caspase-6 VLIT][EDQ][^DENQRKAPGS]D 1221285 1236692 19694615 21111746 Caspase-6 is an effector caspase during apoptosis. Putative role in Huntington’s and Alzheimer’s disease Motif suggestion is based on in vitro data. Optimal described sequence is VEHD For protein substrate see MEROPS or CutDB first draft
[Edit]
[Delete]
LIG_TPR_2 [ILMV][DE]{1,2}[ILMV][DE]$ None Extension of the current over-defined TPR binding motif based on sequence analysis. first draft
[Edit]
[Delete]
LIG_RIP_CTP SD[DE]DMGFGLFD$ 19073700 2JDL 11 residue long C terminal peptide motif of ribosomal stalk proteins which interact with ribosome inactivating proteins (RIP), which in turn leads to depurination of a specific Adenine residue of 28S rRNA and failure of the recruitment of elongation factors to the ribosomal GTPase-associated center, thus inhibition of the translation in the ribosome. first draft
[Edit]
[Delete]
LIG_PUL_PLAA_1 [DE][DE][DE][DE]LY[AGS]$ 3EBB 19887378 Motif in ATPase VCP/p97 that binds to the PUL domain of PLAA. C-termianl motif with acidic extension that fits into a highly positive grove on the PUL domain surface. Involved in the regualtion of Ubiquitination. first draft
[Edit]
[Delete]
LIG_Glycolytic_Aldolase W[DE]{2,3}W 3LGE 20129922 Motif that mediates binding to Aldolase A first draft
[Edit]
[Delete]
LIG_SH3_9 SAMP 18786926 20509626 2RQU a non-canonical SH3 binding motif associated binding to ASAP1 and colocalized at microtubule ends. first draft
[Edit]
[Delete]
LIG_Alpha-synuclein .DVF. 19762560 interaction with coiled coils of Synphilin-1 first draft
[Edit]
[Delete]
LIG_Actin_DMD LK..E[ST] 9883911 actin binding motif found in the Dp71 dystrophin isoform first draft
[Edit]
[Delete]
LIG_ECD_CRF LM..I$ 18801728, 3EHT Extracellular domain (ECD) of corticotropin-releasing factor (CRF) receptor 1 (CRFR1) binds to CRF via its C terminally amidated ligand motif. first draft
[Edit]
[Delete]
LIG_BTB_SMRT [GL][IV][AT]T[IV]KE[AM]GRSIHEIPR 14690607, 1R2B Motif mediating binding of BCL6 BTB domain to SMRT first draft
[Edit]
[Delete]
LIG_EAR 20935498 11487705 EAR motif mediates transcriptional repression of plant genes via recruitment of a histone deacetylase complex, which leads to chromatin modification. first draft
[Edit]
[Delete]
TRG_Golgi 21283809 potential Golgi-retention motif and a number of conserved motifs with unknown function first draft
[Edit]
[Delete]
LIG_SH3_7 [RK][RK].PXXPPXXP..[RK] 17437541 Motif in proline-rich domain of dynamin I that interacts with SH3 domain of endophilin I, consists of tandem core PxxP motif flanked by basic residues; bidirectional binding first draft
[Edit]
[Delete]
LIG_SH3_6 [RK][RK].{9}[RK][RK].PXXPXX[RK]...[RK] 17437541 Motif in proline-rich domain of dynamin I that interacts with SH3 domain of syndapin I, consists of core PxxP motif flanked by basic residues; syndapin I binding sensitive to introduction of negative charges; bidirectional binding first draft
[Edit]
[Delete]
MOD_acetyl_E2ligase_1 [KR]R[IL].KE 21791702 Motif found associated with the acetylation of ubiquitin E2 ligases first draft
[Edit]
[Delete]
LIG_ARM [DEG].EGGGE.D...[FY]....L 20371349, 3L6Y Motif in JMD domain in C-terminal tail of cadherins that interacts with Armadillo repeats in p120 catenin first draft
[Edit]
[Delete]
LIG_BH1_BH3 LA..GD 16475813 Motif of Bid-BH3 that binds to BH1 domain of Bcl-w. This interaction is lost upon Bcl-w lipid binding first draft
[Edit]
[Delete]
LIG_Filamin ..(T)TT.. 20332112,Takala,2008, 2V7D Motif recognized by Filamin. First threonine must not be phosphorylated. Molecular switch. See LIG_Talin and LIG_14-3-3-3 (latter might need updating of regex as does not cover binding motif in integrins mentioned in 18550856) first draft
[Edit]
[Delete]
LIG_Sin3_4 [FLW]..[ILV][ILV]... 21440557, 2L9S PAH motif in Pf1 (Q96QT6) binds to Sin3 (Q60520). Basically extends LIG_Sin3_3. (cave: pdb-structure features human motif but mouse sin3a) first draft
[Edit]
[Delete]
LIG_TF2_FCP1_1 [DE]...[ILMV][AGS]..L..[DE][ILMF] 12732728,12591941, 1J2X Motif in carboxy terminus of FCP1 interacts with carboxy terminus of "Transcription initiation factor IIF subunit alpha" (RAP74). Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains. Might not be linear first draft
[Edit]
[Delete]
LIG_CAVB_AID L.GY..WI 15141227, 1T0J Motif in Voltage-gated calcium channel beta-subunit (Cavb) binds to the conserved alpha-interaction domain (AID) of the same channel Interaction happens between subunits of calcium channel. Motif resides in structured region; found in multiple Voltage-dependent calcium channel subunits. first draft
[Edit]
[Delete]
LIG_FERM_4 MDW.....[LI]F..[LF] 16615918,2YVC Motif that mediates binding to the FERM domain of Radixin found in NHERF-1. Binds different site to PSGL-1, NEP, CD44 and CD43. Nice mutational analysis in paper. first draft
[Edit]
[Delete]
LIG_FERM_3 [KRQ]...Y..[ILV] 12554651,18076570,18753140, 2YVC, 2EMS, 2ZPY, 2EMT Motif that mediates binding to the FERM domain of Radixin found in PSGL-1, NEP, CD44 and CD43. Difficult consensus but all structures overlap the same binding site. first draft
[Edit]
[Delete]
LIG_FERM_2 L...M..L..LM..L..IT 21642953,21321230, 3PZD Large cargo recognition helix in DCC, Ngn and Fz1A that binds to the FERM domain of Myosin-X. first draft
[Edit]
[Delete]
LIG_20S [ILMV]Y.$ 21499243,20019667, 3IPM Binding site on the 20S protesome that is used by both assembly factors such as Pba1-Pba2 and activators such as PAN, Blm10 and PA28. first draft
[Edit]
[Delete]
LIG_CORNRBOX_2 [IL]..[ILV][IL]..[ILVYF] Phelan,2010,3N00 An improved definition of the CoRNbox motif based on structural studies from SMRT and N-Cor. Should update current entry rather than make new entry as they are overlapping. first draft
[Edit]
[Delete]
LIG_RCT L..L[KR].[KR] 21217703,3OWT Helical motif that mediates the binding to the RCT domain of yeast telomeric protein RAP1. Found in TAZ1(1.97uM) and Sir3(2.3uM) overlaps the binding site of a larger higher affinity disordered interface found in TRF2 (16.5nM). first draft
[Edit]
[Delete]
LIG_Caveolin [WFY]....[WFY]..[WFY] 9325253 Motif mediating binding to Caveolin. Found in G-proteins, Src-like kinases, Ha-Ras, and eNOS. Also functions in a anti-parallel conformation. first draft
[Edit]
[Delete]
MOD_phos_AURORA R.([ST]) 21712546,Alexander,2011 Canonical motif phosphorylated by Aurora kinase A/B first draft
[Edit]
[Delete]
LIG_APH1 G...G 18061918, 21507970 conserved alpha helix binding motif; plays a role in maturation of the gamma-secretase complex, but may be involved in other recognitions (see ref2) earns a closer look (Mk) first draft
[Edit]
[Delete]
LIG_AcetylCoA [QR]..G.[GA] 19660096 Conserved core motif responsible for acetyl coenzyme A binding as found in all members of the GNAT superfamily of N-acetyltransferases (GNAT, Pfam: PF00583 Acetyltransf_1) first draft
[Edit]
[Delete]
MOD_HEME CP[ILMVFY] 7835342 Short sequence that has been shown to bind heme and is repeated up to 6 times. first draft
[Edit]
[Delete]
DCK_dephos_PP1_4 F..[KR].[KR] 12115603,20376316 Docking motif for PP1 phosphatase found in several proteins involved in apoptosis such as Bcl-xL. first draft
[Edit]
[Delete]
MOD_SPalmitoyl_X 15189153 Modification site by palmitoylation; may also mask other modifications or binding sites, e.g. by recognins extention of entries class 2 and class 4 first draft
[Edit]
[Delete]
LIG_FERM_ICAM2 R...Y.V...W 12554651, 1J19 Cytosolic side motif in ICAM-2 binds to the PTB-like C domain of the FERM module. Important for membrane-associated cytoskeleton. Peptides with low similarity to ICAM-2 from other proteins also bind in this region of FERM so it may be difficult to define ELM motifs. first draft
[Edit]
[Delete]
LIG_HBOX_DDB1 19966799 13aa structural motif, that must be located inside a disordered region, and which binds to DDB1. It's found in many DDB1 binding proteins but also in viral proteins, such as Hepatitis B virus protein X and parainfluenza virus 5 (formerly called simian virus 5 or SV5) protein V which use it to hijack DDB1. The problem is that it is not rigorously a sequence motif, rather many sequences can adopt this structural motif alpha-helix, but still, the author describes quite a few preferred positions. (Contact: D. Karlin) first draft
[Edit]
[Delete]
LIG_cpSR43_ANK DPLG 18621669, 3DEP The DPLG motif binds L18p to cpSRP43. Part of a chloroplast system inserting light harvesting proteins into thylakoid membranes first draft
[Edit]
[Delete]
LIG_Cdc20_Spo13 L.E...N 17493939 Degron in the yeast meiosis-specific protein SPO13 recognised by the cdc20 subunit of the APC. first draft
[Edit]
[Delete]
MOD_SMAD (S)[IVLM](S)$ 9346908,18387785 C-terminal phosphorylation motif found in receptor-activated Smads. Phosphorylated by TGF-beta1 kinase after its activation first draft
[Edit]
[Delete]
LIG_DHB_DAXX [DE]..[IL]..[WHFY][[WFHY] 21134643 Motifs in Rassf1C mediating binding to the DHB domain of the scaffold protein DAXX. Has structure but not yet in pdb (see paper). first draft
[Edit]
[Delete]
LIG_N_degron_Doa10_Ac ^([MAVSTC]) 20110468 Acetylated N-terminal degron signal recognized by ubiquitin ligase Doa10. Promotes proteosomal degradation. first draft
[Edit]
[Delete]
LIG_AGO_PIWI_1 WG 17891150 Mediates interaction with the Argonaute PIWI domain. Found in Argonaute-interacting protein Tas3. Difficult to annotate. Very variable other than conserved tryptophan. first draft
[Edit]
[Delete]
LIG_BIR_Survivin ^AX(PT) 20705815 Most BIR domain interacting peptides are unmodified but the Survivin BIR domain recognises an N-terminal peptide with phosphothreonine in the third position. first draft
[Edit]
[Delete]
LIG_PKC [YF][SA][VI](Y)[QR].[YF]. 15851033 Phosphotyrosine motif in CDCP1 binding to the PKCd C2 domain. first draft
[Edit]
[Delete]
LIG_PAS_STAT6 L..LL 14757047,12138096 Stat6 motif found in complex wit the PAS domain of NCoA, not the usual nuclear receptor. Indicates a more complex story. first draft
[Edit]
[Delete]
Lig_PAH1_SID 16288918,18089292 Helical motif binding the PAH1 domain of the Sin3 corepressor. There are four PAH domains in Sin3 that are likely to bind helical peptides with different specificities. Reversed orientation binding has been observed for PAH1-binding helices. first draft
[Edit]
[Delete]
LIG_Sap1_Bbox F.L..L 11406578 SRF binding motif with beta-augmentation core. first draft
[Edit]
[Delete]
LIG_Notch DSL 17006545 Conserved N-terminal motif in Notch ligands. first draft
[Edit]
[Delete]
LIG_MYPT1 Y.Y Terrak,2004 Motif on PP1delta reciprocating the RV.F motif on the targeting subunit of MYPT1. MYPT1 also has an N-terminal helical motif interacting with PP1delta. first draft
[Edit]
[Delete]
LIG_TRADD YYD$ 9356494 Tumor necrosis factor receptor-associated death domain protein (TRADD) binding motif in LMP1 first draft
[Edit]
[Delete]
MOD_acetylation 10656693,10607594,9744860,9774110,9809067 Acetylation targets in the nucleus beyond histone tails: p53, HMG I/Y, TCF, etc. first draft
[Edit]
[Delete]
MOD_LammerK (RS)n 11827553,1577277,8772383 Many Lammer kinases (clk1-4, Doa, PK12) phosphorylate (RS)n motifs, regulating splicing. first draft
[Edit]
[Delete]
LIG_RHIM_1 [IV]Q[ILV]G 20346680 RIP homotypic interaction motif found in several programmed necrotic cell injury related proteins. Probably the core of a longer disordered interface first draft
[Edit]
[Delete]
TRG_Paranodin PGY 17093057 Paranodin trafficking repeat motif. first draft
[Edit]
[Delete]
LIG_MIT_MIM2 [ILMV]P[DE]VP[ST]..LP 18606141, 2K3W VPS4 MIT domain binding "MIM2? motif found in a subset of ESCRT-III subunits first draft
[Edit]
[Delete]
TRG_TAT [ST]RR.FLK 16987314 Tat export consensus motif. first draft
[Edit]
[Delete]
TRG_VTS R.L.[EQ] 15591203,15591202 Vacuolar protein export signal. first draft
[Edit]
[Delete]
LIG_TAZ1 LP.L / LPMSP 14594809,12778114,11959977, 1L8C, 1L3E Minimal region of a lager binding motif for the TAZ1 domain in transcriptional adapter protein CBP/PCAF/p300. Complicated binding read [19214187] for explanation. first draft
[Edit]
[Delete]
LIG_RNA_RGG RGG 8290338,12925994,12628254 Motif potentially involved in RNA binding in RGG transcriptional regulators. SMN Tudor domain binds dimethyl-Arg of RGG. first draft
[Edit]
[Delete]
LIG_PHDfingers_H3 ^...K 16728977 NURF and ING types of PHD finger bind histone H3 trimethylated lysine. first draft
[Edit]
[Delete]
TRG_TGN YW 16978406 Retrograde endosome to trans-Golgi network motif. first draft
[Edit]
[Delete]
MOD_methylation 8366133 Modification sites in histone tails and nucleolin. first draft
[Edit]
[Delete]
TRG_RS (RS)n 12215544,1577277,8772383 C-terminal RS domain rich in arginine and serine residues (extensively phosphorylated) that promotes protein protein interactions and directs subcellular localization of SR splicing factors. first draft
[Edit]
[Delete]
TRG_PEXEL_VTS 16046186 Export motif for RBC stage of the malaria parasite. Similar motif in potato blight. first draft
[Edit]
[Delete]
TRG_Parasite_HT R.L.[EDQ] 18621946,19170882 Core motif for N terminal host-targeting (HT) motif composed of 11 amino acids that is found in Plasmodium and other parasites. first draft
[Edit]
[Delete]
TRG_nucleolus 10469277,10050887,9731210 Nucleolar targeting signals. first draft
[Edit]
[Delete]
TRG_Mit 11381593 Mitochondrial targetting peptides. first draft
[Edit]
[Delete]
TRG_ERM-PM RGGKYSV 17995939 Motif responsible for the recruitment of ERM proteins to the plasma membrane in neurogenesis. first draft
[Edit]
[Delete]
TRG_Dendritic LLY..[FYW] 16988049 Dendritic targeting motif. first draft
[Edit]
[Delete]
TRG_chloroplast 10998602 Chloroplast transit peptides. first draft
[Edit]
[Delete]
MOD_Prk1p_1 [LVIM]....(T)G 13679512,11694597,19220811 Motif modified by Prk1p, a yeast kinase localised at cortical actin patches and regulating endocytosis. Substrates include epsins and the Bni1p formin. first draft
[Edit]
[Delete]
LIG_R3IM [DE][DE][DE]EFE[DE] 18775730 Motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. first draft
[Edit]
[Delete]
MOD_MegPhos PPPSP 17555532 Necessary for phosphorylation of Megalin, possibly by GSK3. first draft
[Edit]
[Delete]
LIG_CH_Parvin_Forwards EL..L[LM]..L 18940607, 2VZD Motif mediating binding to the C-terminal calponin homology domain (CH(C)) of alpha-parvin. Possible molecular switch by binding the FAT domain targeting LD motifs of Paxillin. Can bind in an anti parallel orientation. first draft
[Edit]
[Delete]
LIG_LIM [IVLMF]I[IVLMF]R[IVLMF] 16616188 Motif that binds some LIM domains. It is part of larger conserved induced fit module where there might be a second LM02-LIM-binding motif. first draft
[Edit]
[Delete]
LIG_integrin_TGFbeta DL..L 14572313 Integrin binding motif in TGFbeta. first draft
[Edit]
[Delete]
FUN_Aurora 14752279 Double motif in TPX2 regulating Aurora kinase activity first draft
[Edit]
[Delete]
LIG_Integrin_Cell_Adhesion GRKRK 19617625 C-terminal motif of tropoelastin that can bind to cells in a divalent cation dependent manner. Might be an integrin binding motif required for cell adhesion. first draft
[Edit]
[Delete]
LIG_ERCC1 D[ST]G[AG]GF 17948053 Used by XPA to recruits ERCC1-XPF to nucleotide excision repair complexes first draft
[Edit]
[Delete]
FUN_Pin1_Isomerisation P[ST]P 12571275 Pin1 isomerization motif. first draft
[Edit]
[Delete]
FUN_Synaptotagmin KK...K 16987956 Motif required for efficient synaptic transmission. first draft
[Edit]
[Delete]
FUN_UBX QA 16267091 Motif is present in Drosophila Ubx family of HOX genes and with pleiotropic functions in development. first draft
[Edit]
[Delete]
LIG_Abox Littlepage,2002 Another destruction box proposed in Aurora A kinases. first draft
[Edit]
[Delete]
LIG_FERM RSLE 17045809 A FERM domain binding motif in neurofascin. first draft
[Edit]
[Delete]
LIG_Hsc70 QLMLT 17978091,7649995 Motif in the Clathrin Heavy Chain Required for the Hsc70/Auxilin Uncoating Reaction. Sequence bound preferentially by the substrate groove of Hsc70 first draft
[Edit]
[Delete]
LIG_IntA3B1 NVR 17034138 Integrin a3b1 binding motif in thrombospondin. first draft
[Edit]
[Delete]
LIG_FF 12381297,16253993 Phosphorylated and possibly other motifs bind FF domains. Notably the RNA polII CTD. first draft
[Edit]
[Delete]
LIG_Fn_binding LIPAD 19699715 Fibronectin binding motif on the C-terminus of the Leptospira adhesin LigB (LigBCtv), residues 1708-1712 containing sequence LIPAD with an beta-strand and nascent helical structure. first draft
[Edit]
[Delete]
LIG_MDAS_MEF2 12700764 Motif found in the interaction between the MADS box of MEF2b and Cabin1. It aquires an amphipathic alpha-helix structure upon interaction. first draft
[Edit]
[Delete]
FUN_Delta [DE].{2,4}NN[IL] 17006545 Motif conserved between invertebrates and vertebrates in Delta interacting proteins (Serrate/Jagged). Involved in the interaction with the E3 ubiquitin ligases Mib1 and Neur. first draft
[Edit]
[Delete]
LIG_integrin_extracell LDV 19255442 Another extracellular integrin binding motif. first draft
[Edit]
[Delete]
LIG_alphaActin FGPVVA 1142354 Actin binding motif in plaque protein zyxin. Said to require alpha-actinin dimerisation. first draft
[Edit]
[Delete]
LIG_AnkyrinG [VA]P[IL]A..E[SD]D 12716895,12829783 A conserved 9-amino acid motif required for ankyrinG binding. first draft
[Edit]
[Delete]
LIG_AP2alpha_3 W..[FW] 14565955 An AP-2 adaptor interaction motif initially identified in the long-splice isoform of Synaptojanin1. first draft
[Edit]
[Delete]
LIG_betaCatenin_armadillo 11136974,9774110 Motif responsible for the induced fit of 3-segmented IUP regions with the central KEGE-motif. K is not sampled but is acetylated by CBP to regulate the interaction. E/C-Cadherins have similar motif without K so not AC-regulated. Found in TCF/pangolin. first draft
[Edit]
[Delete]
LIG_Calnexin KPKKKKK 14988724 Poly Lysine motif found in Erp57 and responsible for Calnexin binding. Highly conserved in orthologs and always located at the C-terminal end. Might determine the specificity of Calnexin binding versus the protein disulfide-isomerase (PDI). first draft
[Edit]
[Delete]
LIG_chromoshadow_EMSY [VILMF].[VILMF].[VILMF]..[VILMF] 16615912 Motif that binds to HP1 chromoshadow domains from EMSY. first draft
[Edit]
[Delete]
LIG_COPII YNNSNPF, L..LE, D.E 12941276,15093828 Motifs involved in vesicle budding interactions of SNARES with COPII (subunits sec23/24). first draft
[Edit]
[Delete]
LIG_CH_Parvin_Backwards L..L[LM]..LE 18940607, 2VZD Motif mediating binding to the C-terminal calponin homology domain (CH(C)) of alpha-parvin. Possible molecular switch by binding the FAT domain targeting LD motifs of Paxillin. Can bind in an anti parallel orientation. first draft
[Edit]
[Delete]
LIG_CK1 F...F 15121840 Motif in NFAT and Per reported to dock CK1 kinase. Reminiscent of the FXXF motif in the PIF pocket kinases. first draft
[Edit]
[Delete]
LIG_clathr_ClatBox_Cter L[IVLMF].[IVLMF]$ 10449404 Variant clathrin box in yeast found at carboxy termini of e.g. some epsins. first draft
[Edit]
[Delete]
LG_CyclophinA FGP.LP 15845542 Motif proposed to bind Cyclophin A. first draft
[Edit]
[Delete]
LIG_MIT_MIM1 [DE]..L..RL..L[KR] 17928861, 2V6Y VPS4 MIT domain binding "MIM1? motif found in a subset of ESCRT-III subunits first draft
[Edit]
[Delete]
FUN_GPIanchor 11814051,11677780,7482705 Glycosylphosphatidylinositol extracellular plasma membrane anchor. first draft
[Edit]
[Delete]
LIG_Chromatin_H2A-H2B M.LRSG 18688256,16469929 Only 2 instances so far and the motif is completely conserved like this in both. Looking at the structures the SG (both small) is probably just there to allow the angles necessary for a hairpin Chromatin binding peptide, interacts with an acidic pocket formed by a H2A-H2B dimer. first draft
[Edit]
[Delete]
LIG_CKB_1 M.E.L.LC(ST)G.F 15707391,12545175 Triple phosphorylated docking motif in Claspin that binds checkpoint kinase CHK1 first draft
[Edit]
[Delete]
LIG_epitope MYPPPY 11418697 Epitope recognition motif present in CDC28 and conserved accross species. It is involved in the regulation of the immune response of T cells. first draft
[Edit]
[Delete]
LIG_CtBP_2 RRT..PPAL Nardini,2003 Another motif that binds to CtBP. first draft
[Edit]
[Delete]
CLV_GxGD G.GD 20021564 Motif that could be evolutionary conserved to allow cleavage of all possible gamma-secretase substrates. first draft
[Edit]
[Delete]
FAM_apoptotic XX...DD....D Motif found in apoptosis induction proteins: GPP synthases, Nox-a, Bad, Bid, Bik, yt-ppy-a, s81f. first draft
[Edit]
[Delete]
LIG_PUB_PIM_1 DDDLY. wh0cd212664 levofloxacin wh0cd212664 <a href=http://levaquin.us.com/>levofloxacin</a> wh0cd212664 <a href=http://levaquin.us.com/>levofloxacin</a> undergoing annotation
[Edit]
[Delete]
LIG_PLK_PoloBox_1 #.S([ST]).. 12595692,14532005 Phosphoserine site recognised by the Polo-like-kinase via the Polo Boxes. The pSer-peptide binds along the groove between the two Polo boxes undergoing annotation
[Edit]
[Delete]
LIG_PH_Tfb1 [ILVF]..W[ILVF].[DE] 16793543,2GS0 Amphipathic helix motif in P53 that is recognised by the PH domain of the p62 subunit of TFIIH. 3uM and phosphorheostatic binding (pS46 518nM, pT55 457nM and pS46pT55 97nM). undergoing annotation
[Edit]
[Delete]
LIG_Rrp6Rrp47_Mtr4_1 [DE]LFx[VC]F[ED]{1,2} Schuch,2014
4WFD
Exosome associated Rrp6 and Rrp47 modules associate by mutual induced fit into a six-helical intertwined heterodimeric folded domain. The N-terminal helical motif of TRAMP complex factor Mtr4 binds in a surface groove of the preassembled Rrp6-Rrp47 fold. In this way, the TRAMP complex can dock to the exosome as part of its RNA processing function. undergoing annotation
[Edit]
[Delete]
LIG_FAT_Reverse L..L[LM] 18078954,3B71 Motif in CD4 used to bind FAT domain of Focal Adhesion Kinase. Binds the same binding surface as the similarly hydrophobic helical LD motifs of Paxillin but has an anti parallel orientation. undergoing annotation
[Edit]
[Delete]
LIG_CDC20_ABBA_1 [FIVL].[ILMVP][FHY].[DE].{0,3}[DEST] Di Fiore,2015,
He,2013,
4bh6
The ABBA motif binds the CDC20/CDH1 coactivator subunit of the anaphase promoting complex. It is found in a number of key cell cycle proteins. In yeast ACM1, ABBA acts cooperatively with KEN and D-Box motifs to inhibit the APC. It is likely to function similarly in metazoan BubR1. In metazoan cyclin A, the ABBA acts as a degron enabling the cyclin’s destruction in prometaphase, while the APC is otherwise not yet active. undergoing annotation
[Edit]
[Delete]
LIG_BART_Arl2_1 LL[^p][^p]L[^p][^p]LK 19368893,
3DOE
In the GTP bound form, the small GTPase Arl2 expels its N-terminal helix which becomes available to bind the BART domain of BART protein. The Arl2 molecular switching system regulates transport of farnesylated proteins.
undergoing annotation
[Edit]
[Delete]
LIG_CaM_NSCaTE_1 W[^P][^P][^P][IL][^P][AGS][AT] Taiakina,2013, Liu,2012, 18235447,
Liu,2012,
2LQC
Helical motif binding to Calmodulin. Found in N-termini of some calcium channels (CaV1.2/CaV1.3). Presence in long isoforms dependent on alternative translation start. Involved in channel function. Different from the classical Lig_IQ Calmodulin-binding motif. undergoing annotation
[Edit]
[Delete]
LIG_LSD1_SNAG_1 ^mPRsFLv[KR]k 20389281,
21300290,
2Y48
The SNAG domain is a conserved N-terminal motif in some zinc finger and homeobox TFs such as SNAIL, Scratch, GFI1, Gsx1. Inhibits LSD1 demethylation of H3K4 by competitive inhibition of the active site. Has repressive effect. undergoing annotation
[Edit]
[Delete]
LIG_CP L.H.T..R[AP]K 20625546, 3AA6, 3AA1, 3AA0 Motif found in the CARMIL proteins (CARMIL, CD2AP and CKIP-1) that regulate actin capping protein (CP) by removing them from the actin filaments. 10nM affinity. undergoing annotation
[Edit]
[Delete]
MOD_Chk_1 L.R..[ST]. or L.P..[ST]F 12711320, 11821419, 15279791 Several basophilic kinases are reported to have additional hydrophobic residue preferences, including CHK1,2, MK2, PKD. LxRXX(ST) is one such variant p-site motif. Also the +1 position is often hydrophobic. In the case of CHK2, the R can be replaced by P (as in BRCA-1) but then the other positions must be optimal as in LxPxxSF. Therefore it appears that some flexibility in the 3 specificity residues is possible, where, if one position is poor, the others must be optimal. undergoing annotation
[Edit]
[Delete]
DCK_phos_PKA_1 [ILMVFA][ILMVFA]..[ILMVFA]...[ILMVFA][ILMVFA]..[ILMVFA] 20159461, 3IM4 Large amphipathic hydrophobic docking motif for RI and RII regulatory subunits of cyclic AMP dependent protein kinase (PKA). Binds to the D/D dimerisation/docking domain. Found in most AKAP proteins. undergoing annotation
[Edit]
[Delete]
Mod_CDK_Long_2 ...[SP]..K Alexander,2011 Longer version of the cyclin/CDK phosphosite recognised by e.g. CDK1. Lysine is specific in the charge position. undergoing annotation
[Edit]
[Delete]
MOD_HedgehogLipid Pepinsky,1998,Chamoun,2001,11493554 Keeps Hedgehog attached to plasma membrane for short range extracellular signalling. Probably needs its own functional site and different ELM entries. undergoing annotation
[Edit]
[Delete]
LIG_WW_Itch PP.Y....[ST][ILV] 20855944 Extended WW domain binding motif necessary for binding to the 2nd WW domain of Itch. Mutations in the final hydrophobic position have been shown to reduce binding and have been implicated in both Hays-Wells syndrome and Rapp Hodgkin syndrome. undergoing annotation
[Edit]
[Delete]
LIG_WW_Fe65 PPLA 18547980 Putative motif claimed for GSK3beta for binding to Fe65. This interaction is posited to regulate apoptosis and phosphorylation of Tyr 216 of GSK3beta. The sequence region is post-kinase domain but is structured. The PPLA sequence is very poorly conserved too... undergoing annotation
[Edit]
[Delete]
LIG_Centrin_XPC W..L...[IL] 15964821 Motif responsible for the binding of XPC repair protein to Centrin 2. PDB structures available. undergoing annotation
[Edit]
[Delete]
LIG_ANKRIN_ANKRA2_1 PxLPx[IL] Xu,2012,3SO8,3V2O,3V2X,3V31,3V30,3UXG,3UZD Sequence-Specific Recognition of a PxLPxL Motif by an Ankyrin Repeatin ANKRA2. Motif is found in HDAC4, HDAC5, HDAC9, megalin, and regulatory factor X, 5 (RFX5). Annotated as LIG_ANK_PxLPxL_1 fully annotated
[Edit]
[Delete]
DOC_MAPK_RevD_# Garai,2012,
2Y9Q,
3TEI
RevD is the reverse orientation of the MapK docking motif or D motif. It has an amphipathic helical component positioning three hydrophobic residues, a variable spacer and then at least two positively charged residues. Variants of the motif may have preferences for different MapKs such as ERK or p38.
(DOC_MAPK_1)
Annotated as DOC_MAPK_RevD_3 fully annotated
[Edit]
[Delete]
LIG_G3BP_FGDF_1 ##FG[DE]F[DEST] Panas,2015 Motif in USP10 that binds to G3BP as part of stress granule regulation. The system is hijacked by some viral proteins e.g. Semliki Forest virus nsP3 and HSV ICP8 Annotated as LIG_G3BP_FGDF_1 fully annotated
[Edit]
[Delete]
LIG_KLC1_TPR_1 [ILMV].W[ED][DN][ES] Konecna,2006
Morgan,2010
Rosa-Ferreira,2011
Pernigo,2013
3ZFW
Motif in calsyntenin binding to TPR (tetratricopeptide repeat) domains of Kinesin Light Chain1 (KLC1. Also used by Vaccinia Virus. Probably general cargo binding motif, often found paired in cargo proteins. Probably only the W is absolutely conserved, followed by the +1 DE position. Elsewhere charge complementarity may involve multiple alternative positions.
Annotated as LIG_KLC1_TPR_1
fully annotated
[Edit]
[Delete]
LIG_CSL [VILMF]W[VILMF]P 15297877, Wilson,2006, 2FO1 N-terminal motif in Notch, responsible for its interaction with the CSL transcription factor in the nucleus to activate the pathway. Annotated as LIG_CSL_BTD_1. fully annotated
[Edit]
[Delete]
LIG_PALB2_BRCA2_1 WF..L Oliver,2009,
3EU7
Motif in the BRCA2 N-terminus that binds to PALB2. The interaction is required to bring BRCA2 to nuclear foci and is important for DNA double strand break repair. The helical motif core WF..L enters a hydrophobic pocket on the beta-propeller. Additional residues preceding the core also interact on a shallower part of the surface. The N-terminal region of BRCA2 is highly conserved, implying additional interactions are made. This complicates conservation-based estimation of the motif pattern.
Annoteted as LIG_PALB2_WD40_1
fully annotated
[Edit]
[Delete]
LIG__UBA3_E1E2_1 [MLI][ILMF].[VILM].{0,4}K Huang,2004
1TT5
Motif in UBC12 (Neddylation E2) N-terminus that binds in a groove of UBA3 in the E1 complex, determining a neddylation specific interaction. The N-terminal region has an overlapping motif that binds the DCNL co-E3 ligase so this peptide segment must be part of a switching mechanism during neddylation. Spacing of the terminal basic residue needs to be assessed from alignments. Also whether arginine at different spacing will replace lysine.

annotated as LIG_UBA3_1
fully annotated
[Edit]
[Delete]
LIG_PONY_DCNL_1 ^M[ILMF].[IL] Monda,2013
Scott,2011
Huang,2009
4GAO
4GBA
3TDU
N-terminally acetylated motif used during neddylation. When acetylated, NEDD8 E2 ligase N-termini bind the PONY domain of paralogous DCNL1,2,3 NEDD8 co-E3 ligases. Structures of the bound motif available for the NEDD8 E2s UBC12 and UBE2F. The N-terminal region has an overlapping motif that binds the E1 UBA3 so this peptide segment must be part of a switching mechanism during neddylation. Binds in helical conformation so may be possible to extend the motif e.g. to include lysines that make electrostatic interactions but might not be positionally fixed.

annotated as LIG_DCNL_PONY_1
fully annotated
[Edit]
[Delete]
LIG_LRP6_inhibitor NX[VI] Cheng,2011
Ahn,2011
22589387
Bourhis,2011

3SOV
3SOQ
3SOB
1NPE
2JTK
LRP5/6 are the crucial membrane receptor proteins for Wnt Signalling. These proteins form complex with frizzled receptors and allow binding of Wnt which mediates the canonical Wnt Signalling. Antagonists such as Dickkopf (DKK) and sclerostin (SOST) compete with Wnt protein for binding with LRP5 and LRP6. Binding of antagonists halts the canonical Wnt signaling and presents these antagonists as an important therapeutic target. DKK1 can bind independently on two different sites (2:1).
Constructs with mutations in “NXI” motif (N40A, I42E) show decreased binding.

annotated as LIG_LRP6_Inhibitor_1
fully annotated
[Edit]
[Delete]
LIG_GSK3_LRPinhibit_1 PPP[ST]P.[ST] Stamos,2014,
4NM5,
4NM7
The protein kinase GSK3 is active by default. Repeating phosphorylated motifs in the LRP5/6 wnt receptors bind as pseudosubstrates, inhibiting the kinase. As a result, the beta-catenin phosphodegron is no longer phosphorylated, stabilising the transcription factor and allowing its transfer into the nucleus. GSK3 also has an auto-inhibitory N-terminal phosphopeptide which is phosphorylated in different regulatory contexts (e.g. insulin signalling) with a somewhat different, less Pro-rich, sequence preference.

annotated as LIG_GSK3_LRP6_1
fully annotated
[Edit]
[Delete]
LIG_Fzd_KTXXXW KTXXXW 22411803
PMC:3657389
Wong,2003
Punchihewa,2009
Umbhauer,2000

4JKV
The motif is present in C-terminal domain of frizzleds. This motif interacts with PDZ domains of Dishevelled proteins with a low binding affinity. The affinity is affected by the extended regions around motif (N-ter and C-ter both directions). It is known that mutations in this motif lead to disruption of Wnt signalling. This is justified as both Frizzled and Dishevelled are crucial for canonical and non-canonical Wnt signalling pathway. Further this motif is also present in smoothened (SMO) receptors which are having sequence similarity with FZDs. Among the different frizzled types Fz1, Fz2, Fz3, Fz4, and Fz7 have been shown to bind directly with PDZ domain of Dishevelled. The binding of Dishevelled with Fz5 is via a discontinued motif which is spread over C-terminal region of latter. The interaction involves cooperative action of conserved motifs present in third intracellular loop alongwith KTXXXW motif.

annotated as LIG_FZD_DVL_PDZ
fully annotated
[Edit]
[Delete]
LIG_GBD_WASP_1 [ILV][ILVA]..LM..[ILMV] Sallee,2008, Cheng,2008,2K42 Auto inhibitory motif in WASP and N-WASP that binds the autoinhibitory GTPase binding domain (GBD). E. coli EspF(U) also use the motif to deregulate actin assembly. fully annotated
[Edit]
[Delete]
LIG_SUMO_Rev_2 [ED].{0,4}[DE].(K)[FLMVI] Impens,2014
Tammsalu,2014
Hendriks,2014
The reverse sumoylation site is less common (about 20% of SUMO sites) than the canonical site. The requirement for a hydrophobic residue adjacent to the modified K may be weaker. MOD_SUMO_rev_2 fully annotated
[Edit]
[Delete]
LIG_SUFU_Gli_1 [CY]GH[LF} Dunaeva,2003
ZeRuth,2011
responsible for Gli proteins interactions with Sufu. Found in Gli1,2,3 but probably not Gli4. Also found in Glis3 but probably not in Glis1,2. In fly Y is replaced by C. Have not checked animals at higher divergence. LIG_SUFU_1 fully annotated
[Edit]
[Delete]
LIG_RPA_C_ 1 R[QN][RK].[AL] Mer,2000
Ciccia,2009
1DPU

RPA recognition motif found in DNA repair proteins SMARCAL1, Tipin, UNG2, XPA and AD52 LIG_RPA_C_Fungi, LIG_RPA_C_Insects, LIG_RPA_C_Plants, LIG_RPA_C_Vert fully annotated
[Edit]
[Delete]
LIG_SPRY_SPSB [DE][IL]NNN Filippakopoulos,2010, 2V24 Motif found in PAR-4/VASA mediating binding to the SPRY domain of the SPSB family of E3 ubiquitin ligases and their orthologue GUSTAVUS LIG_SPRY_1 fully annotated
[Edit]
[Delete]
Doc_Pex_5 LVAEF Neuhaus,2014

4BXU
LVAEF is a Pex14-binding motif located at the N-terminal domain of the human PTS1 (Peroxisomal targeting signal 1) receptor Pex5. It has been suggested that the motif represents a docking site for cargo loaded receptor. Mutating motif to alanines affects the import of proteins into peroxisomes. Evolutionary conserved consensus sequence of the motif is LVXEF. The motif is not found in plant and yeast Pex5 but is present in Pex5 from a number of filamentous fungi. Binding kinetics of LVAEF motif are faster than the canonical diaromatic pentapeptide motif (WXXX[FY]) present in Pex5. This suggests that site might assist in establishing the first contact of Pex14 with PTS1 receptor. LIG_Pex14_3 fully annotated
[Edit]
[Delete]
LIG_LIR WxxL or [WYF]xx[LIV] Rozenknop,2011 LC3-interacting region (LIR) might link ubiquitinated substrates that should be degraded to the autophagy modifiers in the autophagosome membrane LIG_LIR_Gen_1; LIG_LIR_Apic_2, LIG_LIR_LC3C_4, LIG_LIR_Nem_3 fully annotated
[Edit]
[Delete]
LIG_CID_NIM_1 DDDEDgyNPYTl Tudek,2014
2MOW
Motif in Trf4 that binds to the CID domain of Nrd1. Links the TRAMP complex to the NNS complex involved in sn/snoRNA production. NIM acts as a molecular switch, competing for binding with the RNA Pol CTD phosphomotif YSPTSPS. Interaction defined in yeast. Alignment needed to derive the motif conservation in fungi, metazoa etc. Not to be confused with the CNOT1 binding NIM motif. LIG_CID_NIM_1 fully annotated
[Edit]
[Delete]
DEG_Kelch_KLHL2_1 E.EE.E[AV]DQH Takahashi,2013 WNK kinases are involved in osmotic regulation and may be mutated in certain diseases that show a hypertension phenotype. An Acidic degron motif is highly conserved in vertebrate WNKs and is reported to target them for destruction by the cullin/KLHL2,3 kelch proteins, the latter designated as E3 ligases. WNK kinases disregulated for proper destruction can cause hypertensive disease.
Motif very strongly conserved in 4 vertebrate paralogues. Should look deeper into metazoa for motif definition. DEG_Kelch_KLHL3_1 fully annotated
[Edit]
[Delete]
DEG_Kelch_KEAP1_1 D.ETGE Padmanabhan,2006, Lo,2006, Lo,2006, 2FLU Oxidative stress response degron motif in the Nrf2 TF binding to the Kelch beta propeller domain in E3 ligase Keap1. A second Nrf2 motif LxxQDxDLG may bind the same Kelch domain with lower affinity. PGAM5 has an NxESGE and is also a Keap1 substrate. DEG_Kelch_Keap1_1 fully annotated
[Edit]
[Delete]
LIG_APCC_Dbox_3 .R.{2,3}L.{1,3}[LIVM] Hames,2001
11285280
Extended Dbox also tends to have further residues upstream that are required for recognition DEG_APCC_DBOX_1 fully annotated
[Edit]
[Delete]
Mtr4-binding motif in Air2 GRYFG Falk,2014
4U4C
One of several peptide motifs used in assembly of the TRAMP complex in yeast. Docks the zinc knuckle protein Air1/2 onto the helicase Mtr4. TRAMP is involved in nuclear surveillance of ncRNAs.
fully annotated
[Edit]
[Delete]
DEG_SPOP_SBC_1 [AVP].S[ST][ST] Zhuang,2009
Zhang,2009
3IVQ
The SPOP Cullin E3 ligase recognizes an unusual ST-rich peptide motif in substrate proteins. The phosphorylated site does not bind SPOP, offering possibilities for PTM regulation. Substrates include GLI3 and MacroH2A. fully annotated
[Edit]
[Delete]
DOC_Cks1_1 [PLFWY][^P](T)P. McGrath,2013, Koivomagi,2013, 4LPA Cks1 co-regulates CDK activity. A subset of pTP sites can be bound in CDK substrates or other regulators. CDK site targeting becomes more precise than with cyclin docking alone. Only described so far in the yeast experimental system but Cks1 homologues are found in e.g. vertebrates too. fully annotated
[Edit]
[Delete]
Doc_PP2A_KARD_1 LS.I[IML]E.S....T Suijkerbuijk,2012,Kruse,2013,Xu,2013 The card motif in BUBR1 recruits the phosphatase PP2A during cell cycle. This is important for mitotic progression. The motif is considered to be triply phosphorylated to bind PP2A.
fully annotated
[Edit]
[Delete]
Doc_GSK3_Axin_1 P[^P][^P]Fa[^P][^P]Li[^P][^P]L[^P][^P][VIL] Dajani,2003
1O9U
Helical motif in Axin protein docks GSK3beta into the Axin-scaffolded complexes. Docked GSK3beta can mark beta-catenin for destruction. The FRAT helical motif binds the same surface but the details are different. fully annotated
[Edit]
[Delete]
LIG_MTR4_Trf4_1 NxDFIx[FL] Falk,2014
Losh,2015
4U4C
One of several peptide motifs used in assembly of the TRAMP complex in yeast. Docks the poly(A)polymerase Trf4/5 by beta augmentation onto the helicase Mtr4. TRAMP is involved in nuclear surveillance of ncRNAs.
Motif pattern should be possible to define for metazoan equivalent with core EQxDF[IL]P fully annotated
[Edit]
[Delete]
LIG_ALG2 PPYP.{1,4}YP Suzuki,2008, 2ZNE motif in Alix that binds to ALG-2 in a calcium-dependent manner (allosteric opening of hydrophobic pocket on ALG-2); similar sequence present in annexin A7 and A11, and in TSG101 fully annotated
[Edit]
[Delete]
LIG_AIM [WY]..[ILV] Noda,2010,3dow,2zzp,2zjd,2zpn Atg8-family interacting motif (AIM) found in Atg19, p62, Atg4B and Calreticulin, involved in autophagy related processes fully annotated
[Edit]
[Delete]
LIG_GABARAP W.FL Thielmann,2009
Mohrluder,2007
17916189
3DOW
GABAA receptor binding to clathrin and calreticulin. possibly linked to trafficking fully annotated
[Edit]
[Delete]
DCK_dephos_PP1_2 R..Q[VIL][KR].[YW] Terrak,2004,Hendrickx,2009, 1S70 Docking motif, referred to as the MyPhoNe motif, for PP1 phosphatase found in Myosin phosphatase-targeting subunit 1. fully annotated
[Edit]
[Delete]
LIG_CNOT1_NIM_1 F..W.DY..L Bhandari,2014, 4CQO The NIM motif (Not1 Interacting Motif) is conserved in the vertebrate RNA-binding paralogues, Nanos1, -2, -3. It binds the SHD domain of CNOT1, thereby recruiting the CCR4-NOT deadenylase complex. Nanos is a classical developmental regulator affecting posterior pattern formation in Drosophila. It is an RNA-binding protein affecting post-transcriptional mRNA regulation. The CCR4-NOT deadenylase complex catalyses the removal of poly(A) tails. The Nanos/CCR4-NOT interaction therefore modulates translational repression. fully annotated
[Edit]
[Delete]
LIG_PP2B_2 .L.VP Rodriguez,2009, Roy,2009, Liu,2001, 10202017, Martinez-Martinez,2006, Park,2000, Dougherty,2009, Mehta,2009, Blumenthal,1986, Grigoriu,2013,
4F0Z
Secondary, lower affinity(?), docking motif for the calcium-activated phosphatase Calcineurin/PP2B. Found in NFATc1-4, KSR2, PRKAR2A and yeast RCN1. ("PVIVIT") is the other Calcineurin binding motif. High affinity motifs may have a large hydrophobic residue preceding the L. The solved motif structure has lysine replacing proline. Binds activated form of Calcineurin; requires both catalytic CNA and regulatory CNB subunits for binding (binding site was identified in silico as hydrophobic cleft formed at interface of preassembled CNA and CNB and confirmed with the solved structure). fully annotated
[Edit]
[Delete]
FUN_N-end_rule_pathway Tasaki,2007 N-terminal ubiquitin mediated destruction system. May be ancient. Might not be a single motif but a combination of post translational modifications. fully annotated
[Edit]
[Delete]
TRG_ER_diArg_2 .RR. 14527949 Generic di-arginine ER retention motif fully annotated
[Edit]
[Delete]
LIG_TRAF2_3 P.Q.[ST] 12917691
Ye,1999
Ye,1999
1CZY
1QSC
1CZZ
Slight variant of LIG_TRAF motifs already in ELM. fully annotated
[Edit]
[Delete]
FUN_RANK P[VILF]QE 16260781 Motif in cytosolic part of RANK (TNFR11A) reported to mediate osteoclast formation, survival and function. Also found in TNFR5. Specific subset of LIG_TRAF2 with improved motif definition. PVQE is absolutely conserved twice in RANK and once in TNFR5. The reported PFQE is unconserved. Therefore the motif is probably an exact match to PVQE

Ligand domain is not known yet?
fully annotated
[Edit]
[Delete]
LIG_WD40_WDR5win_1 G[GASC]AR....[FLYM] Dharmarajan,2012,
18829457,
18829459,
16829960,
3UVN,
3UVL
The Win motif has a turn of helix with an Arg residue that binds deep into the wD40 domain axis. Found in WDR5-interacting proteins including SET1A and MLL2 Small sidechains precede the R. Pro should be disfavoured at several positions of the motif due to backbone H-bonding requirements. A preference for a hydrophobic residue is found +5 of the R. fully annotated
[Edit]
[Delete]
LIG_WD40_WDR5_2 .VDV[TV] Odho,2010
2XL2
The VDV motif is found in RbBP5 and interacts with an edge cleft of the WD40 domain in WDR5.
This interaction surface is different from the canonical axial site (in this case bound by the Win motif). RbBP5 is found in a number of chromatin complexes including SET1 and MLL.
Core motif may be preceded by several negatively charged residues. The core D does not directly bind WDR5 but makes an internal charged interaction that is probably important for the peptide geometry.

fully annotated
[Edit]
[Delete]
DCK_dephos_PP1_3 [GS]IL[RK] Wakula,2003 Docking motif, referred to as the SILK motif, for PP1 phosphatase found in NIPP1 fully annotated
[Edit]
[Delete]
LIG_CASK_CID_1 E.[IV]W[IV].R Stafford,2011 Docking motif in Caskin1, Mint1 and TIAM1 that binds to the CASK hub protein involved in brain, synapse, cell polarity. fully annotated
[Edit]
[Delete]
LIG_N_degron_UBR_type1 ^[RKH][^P] Matta-Camacho,2010,Choi,2010, 3NY1, 3NIT Primary N-terminal basic degron. Likes hydrophobics in second position. Lysine binds with the highest affinity (~20uM). N-degrons are N-terminal proteosomal degradation targeting motifs recognised by UBR domains of the Ubiquitin recognin (UBR) family. Several N-degrons are known, defined as primary (type 1 & type 2), secondary and tertiary. fully annotated
[Edit]
[Delete]
LIG_N_degron_UBR_type2 ^[FLWYI] Tasaki,2007 Primary N-terminal bulky hydrophobic degron. N-degrons are N-terminal proteosomal degradation targeting motifs recognised by UBR domains of the Ubiquitin recognin (UBR) family. Several N-degrons are known, defined as primary (type 1 & type 2), secondary and tertiary. fully annotated
[Edit]
[Delete]
LIG_N_degron_UBR_secondary ^[DEC] Tasaki,2007 Secondary N-degron, arginylated (addition of an N-terminal arginine) by Arg-tRNA-tranferase. Cysteine must first be oxidised into Cys-sulfinic acid before arginylation. Once arginylated the motif is recognised as a type1 N-degron. N-degrons are N-terminal proteosomal degradation targeting motifs recognised by UBR domains of the Ubiquitin recognin (UBR) family. Several N-degrons are known, defined as primary (type 1 & type 2), secondary and tertiary fully annotated
[Edit]
[Delete]
LIG_N_degron_UBR_tertiary ^[NQ] Tasaki,2007 Tertiary N-degron, deamidated by N-terminal amidohydrolase. Deamidation creates the secondary destabilising N-terminal residues Asp and Glu, which in turn are arginylated (addition of an N-terminal arginine) by Arg-tRNA-tranferase to create a primary N-degron. N-degrons are N-terminal proteosomal degradation targeting motifs recognised by UBR domains of the Ubiquitin recognin (UBR) family. Several N-degrons are known, defined as primary (type 1 & type 2), secondary and tertiary. fully annotated
[Edit]
[Delete]
LIG_TNK_1 R..PDG 22153076,Guettler,2011 Tankyrase 1 & 2 (TNKS, TNKS2) bind to a common set of proteins including IRAP, TAB182 and FBP17, all of whom share this common motif. Annotated as LIG_TNKBM_1 fully annotated
[Edit]
[Delete]
LIG_APCC_Cbox DR[YF]IP.R Schwab,2001 motif required for association with APC/C, conserved in Cdc20-related proteins annotated as LIG_APCC_Cbox_1 / LIG_APCC_Cbox_2 fully annotated
[Edit]
[Delete]
LIG_APCC_#R_1 .[LM]R$ Sedgwick,2013, Hayes,2006 Some proteins interact with APC/C via C-terminal LR or MR motifs. These include Nek2A and Kif18A. The MR motif in Nek2A allows it to be destroyed by APC/C in a checkpoint independent manner annotated as LIG_APCC_TPR_1 fully annotated
[Edit]
[Delete]
LIG_APCC_IR_1 .IR$ Burton,2005,Passmore,2003,Vodermaier,2003 The C-terminal IR motif anchors CDC20 and CDH1 D/KEN box adaptors as well as APC10 to the main APC/C complex. Recognised by a groove in TPR repeats. annotated as LIG_APCC_TPR_1 fully annotated
[Edit]
[Delete]
LIG_SCF_TIR1 GWPPV 15295098
Ramos,2001
Parry,2006
Tan,2007
2P1Q
A degron motif found in plants responsible for the degradation of members of the Aux/IAA family of transcriptional repressors fully annotated
[Edit]
[Delete]
LIG_PAM2_2 W..EF.PG..W.... Jinek,2010,Kozlov,2010, 2X04, 3KTP binding motif in GW182 family proteins for binding with PABC domain of PABP1, essential for microRNA-mediated translation repression and deadenylation fully annotated
[Edit]
[Delete]
LIG_PAM2 [FPLV][^P][IPVTA].A..F.P Kozlov,2004,Albrecht,2004,Kozlov,2010 PABC/MLLE2-binding motifs involved in translational regulation. fully annotated
[Edit]
[Delete]
LIG_SCF_COI1 RR..L..FL Chini,2007
Sheard,2010
3OGM
Thines,2007
Katsir,2008
Gfeller,2010
a degron found in plants associated with the Jasmonate family of transcription repressors. fully annotated
[Edit]
[Delete]
LIG_NBox_RRM_1 Cukier,2010 Ala-rich amphipathic helical motif in FBP and homologues binding to the helical side of FIR RRM2 which has a shallow hydrophobic face. Part of FIR mediated c-myc transcriptional control. fully annotated
[Edit]
[Delete]
LIG_MYND_2 PPPLI Liu,2007, 2ODD Motif that mediates the interaction between MYND domain of AML1/ETO and co-repressors SMRT and N-CoR. fully annotated
[Edit]
[Delete]
LIG_MYND_PHD2_1 P.LE Song,2013 Variant MYND binding motif found in the HSP90 co-chaperones p23 and FKBP38 interacting with PHD2 MYND domain Interaction is part of HIF1-alpha hydroxyproline oxygene sensing system fully annotated
[Edit]
[Delete]
MOD_phos_NEK2 [FLM][^P][^P]([ST])[^DEP][HR] Alexander,2011 Canonical motif phosphorylated by NEK2 MOD_NEK2_1, MOD_NEK2_2 fully annotated
[Edit]
[Delete]
LIG_CEP55 GPP...Y Lee,2008, 3E1R motif in Alix and TSG101 that interacts with coiled coil in CEP55; motif overlaps with motif for binding to ALG-2 fully annotated
[Edit]
[Delete]
TRG_ER_diArg_1 R.{0, 1}R Michelsen,2005 ER retention/retrieving signal found in ER membrane proteins (cytoplasmic side) should replace current TRG_ER_diArg_1 fully annotated
[Edit]
[Delete]
LIG_SCF_SKP2 Hao,2005 Complex phosphopeptide motif binding to the assembled dimer of Skp2 and Cks1 (SCF components), in the ubiquitin degradation process. annotated as LIG_SCF_Skp2-Cks1_1 fully annotated
[Edit]
[Delete]
LIG_PIKK_1 [DEN][DEN].{2,3}[ILMVA][DEN][DEN]L.{0,20}$ Falck,2005 Docking motif for PIKK kinases family found in DNA damage proteins Nbs1, ATRIP and XRCC5. alias DCK_phos_PIKK_1 fully annotated
[Edit]
[Delete]
LIG_eIF4E_1 Y....L[VILMF] Fierro-Monti,2006 Motif present in some interacting partners of eIF4E. annotated as LIG_eIF4E_1 fully annotated
[Edit]
[Delete]
LIG_eIF4E_2 Y.PP.[ILMV]R Shih,2008 Mediates binding to the dorsal surface of eIF4E. Found in DDX3, eIF-3G and eIF-2A annotated as LIG_eIF4E_2 fully annotated
[Edit]
[Delete]
MOD_LATS_1 H.R..[ST] Zhao,2007 Mammalian tumour suppressors LATS1 and 2 are AGC group kinases involved in the Hippo pathway. Similar kinases are conserved in other Eukaryotes. Known substrates YAP1 and WWTR1 (TAZ) have multiple HxRxxS motifs that are phosphorylated by the LATS kinases. Thus these kinases appear to have a target specificity that is distinct from other AGC group kinases. annotated as MOD_LATS_1 fully annotated
[Edit]
[Delete]
LIG_SUMO_SBM V.[VI][VI] Song,2004, Hecker,2006, Berndt,2009 Motif reported to bind SUMO present in RanBP2, PML, among cothers. annotated as LIG_SUMO_SBM_1 and LIG_SUMO_SBM_2 fully annotated
[Edit]
[Delete]
CLV_Separin S[HILMV][DE].GR[RKS] Sullivan,2001 Recognition site for cleavage by Caspase-like protease Separin. annotated as CLV_Separin_Metazoa and CLV_Separin_Fungi fully annotated
[Edit]
[Delete]
LIG_RhoGAP_OCRL_1 F...H..[ILVFY] PDB:Pirruccello,2011,3QIS F&H motif mediates binding to the RhoGAP domain of OCRL. Found in Ses1, Ses2 and APPL1. annotated as LIG_OCRL_FandH_1 fully annotated
[Edit]
[Delete]
LIG_Pex3P_1 L..LL...L..F Sato,2010 Large induced hydrophobic helix mediating binding to the Pex3p protein, found in Pex19p. annotated as TRG_PEX_3 fully annotated
[Edit]
[Delete]
Lig_CAP-Gly_2 W[KR][ED]GCY$ van der Vaart,2011,3RDV C-terminal Tyr-based motif in SLAIN2 that binds the CAP-Gly motif of CLIP-170 as part of MT regulation by +TIP interaction networks. Lig_CAP-Gly_CLIP170_2 fully annotated
[Edit]
[Delete]
CLV_Caspase3-7 D..D[AGS] 12107159 Caspase-3/Caspase-7 cleavage motif. fully annotated
[Edit]
[Delete]
LIG_SCF_Cks1_1 .E.(T)P. Hao,2005, 2AST Phosphodegron in P27kip1 which must be targeted for destruction by SCF ubiquitination to allow the cell cycle progression fully annotated
[Edit]
[Delete]
LIG_HCF-1 [ED]H.Y Luciano,2003 HCF-binding motif, to bind to a six-bladed β-propeller domain at the N terminus of HCF-1 fully annotated
[Edit]
[Delete]
LIG_RB_pocket [IL]..L[YF] Liu,2007,Xiao,2003 Binding to the E2f binding pocket between the Rb-A and Rb-B domains fully annotated
[Edit]
[Delete]
LIG_SPAK-OSR1 RF.V Villa,2007 Docking motif in substrates of OSR1 and SPAK kinases that binds to the CCT domain. fully annotated
[Edit]
[Delete]
LIG_Integrin_isoDGR NGR Spitaleri,2008 Integrin aVB3 binding motif in the 5th type I repeat of fibronectin. Aspargine deamidation at an NGR peptide generates the functional isoDGR binding motifs. Binds with comparable affinity to the canonical RGD peptide that binds the same site. fully annotated
[Edit]
[Delete]
LIG_Actin_WH2_1 [ILMV][ILMV]..I.{4,7}L[KR][KR][ILMVT] Paunola,2002,2A3Z,2A40,2A41,2D1K,2VCP,3MN5,3MN7 Long actin binding motif, probably too large to be defined as an ELM but if we put LIG_Actin_RPEL_1 in then this will also be entered. fully annotated
[Edit]
[Delete]
LIG_Actin_RPEL_1 L..[KR][IL]..R[PQ]...[ED]L..[RK].[ILMV][ILMV] Mouilleron,2008,2V52 Bipartite helical motif mediating binding to the subdomain 1-3 hydrophobic cleft and a ledge on subdomain 3 of G-actin. Probably to large to be defined as an ELM but may be seen as a bipartite motif with possible unknown monopartite motif-containing binding partners binding one of the two interfaces. fully annotated
[Edit]
[Delete]
LIG_PIF F..F or F..F([ST]) Biondi,2004 Binding motif in PDK1, PKA, PKG, PKC etc. AGC kinase pockets, usually in cis, except in PDK1 where there it is a trans docking motif. fully annotated
[Edit]
[Delete]
TRG_ER-exit LLV 19535327 A highly conserved motif near the C-terminus that dictates ER exit and cell-surface expression of NKCC2. Although very conserved, the motif seems to be quite specific for NKCC2 and not very general: several reports show that deletion/mutation of this motif in other receptors do not retain the protein in the ER. (see student's report) not annotatable
[Edit]
[Delete]
FAM_TypeIII W...E 16413475 Motif present in signalling effectors used by pathogens to mimic activated Ras-like cellular GTPases. no linear motif: Motif resides (in all checked instances) in a globular region (helix). not annotatable
[Edit]
[Delete]
LIG_SH2_SRC11 P[KR] 123123 hello hello deleted
[Edit]
LIG_SH2_SRC1 TTT 123123 123safd sadfsafd deleted
[Edit]
LIG_SH2_SRC3 P..P[KR]T 123123 lkjss lkjsdf deleted
[Edit]
LIG_KLC1 [ILMV].WD.. Konecna,2006 motif mediating binding to the tetratricopeptide repeats of KLC1 duplicate of LIG_KLC1_TPR_1 deleted
[Edit]
LIG_Wnt LT...W Umbhauer,2000 Motif found in Frizzled (Receptor of Wnt) and involved in the activation of the Wnt/beta-catenin signaling pathway. Mutations in the fixed positions induce the expression of the Wnt target gene siamois. see LIG_Fzd_KTXXXW deleted
[Edit]
LIG_APCC_KILR KILR Izawa,2012 Motif in Cdc20 that mediates binding to APC/C subunits. The main determinants are the I and L residues; mutation of the basic residues decreases but not abrogates binding to both APC/C and Mad2. This same sequence also mediates binding of Cdc20 to Mad2 (see LIG_MAD2); preventing the motif to bind APC/C by hiding by Mad2 would be one of several mechanisms involved in regulation of APC/C activity and substrate specificity by the spindle assembly checkpoint. Possible interactor is Cdc23 TPR region, see Matyskiela,2009. deleted
[Edit]
LIG_VHS D..LL 20502673 1ELK 10985773 The VHS domain of GGA proteins binds to an acidic di-leucine motif in the cytoplasmic domain of sorting receptors including the mannose 6-phosphate receptor. duplicate of TRG_LysEnd_GGAAcLL_1 deleted
[Edit]
LIG_BCL2 L..I[AG]D.[ILV] 20502673 1BXL
Sattler,1997
Bcl2 motif deleted
[Edit]
LIG_HIV1-GP41 H..NPF 16904109 HIV-1 gp41 core-binding motif. deleted
[Edit]
CLV_C14_Caspase-8-10 [^RK][EDQ].D 1221285 1236692 19694615 10964557 10508785 Caspase-8 and -10 are the initiator caspase in the extrinsic apoptotic pathway and cleaves executor caspases. Motif suggestion is based on in vitro data. Optimal described sequence is LETD. For protein substrate see MEROPS or CutDB No in vitro data for caspase-10 but cleavage motif LEXD in literature is described. deleted
[Edit]
LIG_CD40 EQLKKSKTL 21998326 Linear peptide in an exposed loop mediates interaction between CD40L and Mac-1 might be too specific paper not freely accessible deleted
[Edit]
LIG_PTB_splicing [SG][IL]LG..P Rideau,2006 Motif essential for splicing repressor activity found in cofactors of the PTB regulatory splicing repressor (Polypyrimidine tract-binding protein). deleted
[Edit]
LIG_MOB1_1 [YF].([ST])[AV][AV] 23579499
4JIZ
Interaction in the mitotic exit network (MEN) or HIPPO pathway. Cell cycle motif modified by Cdc15 kinase and then bound by Mob1 Should be possible to derive motif by alignment due to deep conservation in eukaryotes. But should check if yeast and metazoan motifs can be represented together. annotatable
[Edit]
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement
feedback@elm.eu.org