Currently 226 candidates need annotation:
| Identifier | Model | References | Description | Notes | Status | |
|---|---|---|---|---|---|---|
| LIG_LIR | WxxL or [WYF]xx[LIV] | PMID:21620860 | LC3-interacting region (LIR) might link ubiquitinated substrates that should be degraded to the autophagy modifiers in the autophagosome membrane |
first draft |
[updated] |
|
| TRG_NES_CRM1_2 | L.{2,3}L.L | PMID:11074002 | very general NES |
first draft |
[updated] |
|
| LIG_PTB_Talin | SPLH | PDB:1Y19 , PDB:2G35 PMID: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 |
[updated] |
| LIG_APCC_Dbox_3 | .R.{2,3}L.{1,3}[LIVM] | PMID:11742988 PMID:11285280 |
Extended Dbox also tends to have further residues upstream that are required for recognition |
first draft |
[updated] |
|
| CLV_C14_Metacaspase | PMID:17028019, PMID:18005666, PMID:19820703, PMID: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 |
[updated] |
|
| LIG_TRAF2_3 | P.Q.[ST] | PMID:12917691 PMID:10518213 PMID:10518213 PDB:1CZY PDB:1QSC PDB:1CZZ |
Slight variant of LIG_TRAF motifs already in ELM. |
first draft |
||
| TRG_LysEnd_APsAcLL_2 | [DERQ].{2,4}L[LVI] | PMID:18315530 PMID:10611976 |
Slight variation of TRG_LysEnd_APsAcLL_1 |
first draft |
||
| TRG_MLS | PMID:22178138 PMID:10837244 PMID:16616497 |
The N-terminal Mitochondrial localisation signal recognised by Tom70. | Could not define regular expression |
first draft |
||
| LIG_IQ_3 | [FILV]Q...[RK]G...[RK]..[FILVWYM] | PMID:9141499 PMID:8805510 PMID:8127365 PMID:12351846 PMID:11911888 |
extended IQ motif |
first draft |
||
| LIG_IQ_2 | [FILV]Q...[RK] | PMID:9141499 PMID:8805510 PMID:8127365 PMID:12351846 PMID:11911888 |
IQ-like motif. |
first draft |
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| LIG_SCF-TrCP1_2 | [EDST][ESTD][GAS].{2,3}[STD] | PMID:19150432 PMID:14676825 PMID:15070733 PMID:15845771 PMID:18354483 PMID:17387146 PMID:18378670 PMID:15917222 PMID:15767683 |
non-canonical variants of the LIG_SCF-TrCP1_1 |
first draft |
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| LIG_PCNA_2 | [ILVM][^ILVM][DHFM][ILVM] | PMID:11682605 | slight variation on original PCNA motif |
first draft |
||
| LIG_BIR_internal | A.[AP]. | PMID:14523016 | Internal BIR-binding site. In this case, precursor mitochondrial localisation signal is removed exposing BIR site |
first draft |
||
| LIG_PI(4,5)P2 | [KR].{3,4}K.[KR][KR] | PMID:9891784, PMID:15483625 | lipid binding motif for PI(4,5)P2 |
first draft |
||
| LIG_Filamin_2 | Y..A[VIL]...[VIL] | PMID:16455489 PDB:2BRQ |
Based on integrin binding to filamin | No mention of importance of threonines defined in LIG_Filamin |
first draft |
|
| LIG_TNK_1 | R..PDG | PMID:22153076, PMID:22153077 | Tankyrase 1 & 2 (TNKS, TNKS2) bind to a common set of proteins including IRAP, TAB182 and FBP17, all of whom share this common motif. |
first draft |
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| LIG_CYCLIN_2 | L..P[ILVMF].[ILVMF] | PMID:21945277 | These sites bind preferentially to Cln2 and enhance phosphorylation of Cdk substrates in a cyclin-specific manner. | found in yeast |
first draft |
|
| LIG_TPR_4 | [ST].[ST] | PMID:21454478 PDB:3Q4A |
phosphorylated version of LIG_TPR found in Smad 1/5 |
first draft |
||
| LIG_TPR_3 | K[IL].{0,2}Q | PMID:18759457 PMID:17942943 |
internal TPR binding motif with similatities found in androgen receptor and vpu | unsure of veracity |
first draft |
|
| TRG_multiple | PMID: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 |
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| LIG_MIU | [DE][LIVY].[LIV]A..[LIVY]..[DE]{DE] | PMID:16499958 PDB:2C7N PDB:2C7M PMID:19217402 |
MIU (motif interacting with ubiquitin; also known as IUIM or inverted UIM) |
first draft |
||
| LIG_TAZ2 | F.[DE]...L | PMID:10196247, PMID:19217391, PMID:16319895, PDB:2KJE , PDB: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 |
|
| LIG_DUIM | [DE].[LIVY]..A[LIVYM]A.S.[SA][DE] | PMID:16462748 PDB: 2D3G | double sided ubiquitin interacting motif |
first draft |
||
| LIG_UIM | [DE][DE]..[ILVY]..A[ILVY].S.. | PMID:16462748 PMID:12970172 PDB: 1Q0V PDB: 2D3G PMID:12750381 PDB:1O06 | Ubiquitin interacting motif |
first draft |
||
| MOD_N-GLC_Bacteria | [DE].(N)[^P][ST].. | PMID:16619027 PMID:21209858 PMID:20523900 PMID:20847188 PMID: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 |
|
| MOD_N-GLC_3 | NG. | PMID:20510933 PMID:21978957 | Non-canonical N-glycosylations sites found in the mouse glycoproteome |
first draft |
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| MOD_N-GLC_4 | N.V | PMID:20510933 PMID:21978957 | Non-canonical N-glycosylations sites found in the mouse glycoproteome |
first draft |
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| MOD_LATS_1 | H.R..[ST] | PMID:17974916 | 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. |
first draft |
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| LIG_CASK_CID_1 | E.[IV]W[IV].R | PMID:21763699 | Docking motif in Caskin1, Mint1 and TIAM1 that binds to the CASK hub protein involved in brain, synapse, cell polarity. |
first draft |
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| LIG_PCNA_PIP_2 | ...[LIM][DE].[FHY][FHY]. | PMID:19208623, PDB:2ZVM , PMID:20606006, PMID:19081076 | 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 |
|
| CLV_C14_Caspase-1 | [WFYML][^P].D | PMID:1221285 PMID:1236692 PMID: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 |
|
| LIG_WW_Nedd4L | .(S)P.L(S)PN | PMID:21685363, PDB: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 |
||
| TRG_ER_diArg_1 | R.{0,1}R | PMID:16065065 | ER retention/retrieving signal found in ER membrane proteins (cytoplasmic side) | should replace current TRG_ER_diArg_1 |
first draft |
|
| MOD_Geranyl_CAAXbox_1 | (C).[LIVM][ILMV]$ | PMID:12702202 | Motif modified by Geranylgeranyltransferase I (GGT1). | Should replace current MOD_CAAXbox to define specificity. |
first draft |
|
| MOD_Farnesyl_CAAXbox_1 | (C).[LIVM].$ | PMID:12702202 | Motif modified by Farnesyltransferase. | Should replace current MOD_CAAXbox to define specificity. |
first draft |
|
| LIG_DCUN1_1 | (M)[IL].L | PMID:21940857 PDB:3TDZ | Acetylated N-terminal methionine motif that mediates binding to the DCUN domain of E3 ligase DCN1 found in E2 ligase Ubc12. |
first draft |
||
| LIG_LCK_1 | C.CP | PMID:14500983 PDB:1Q69 PDB: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 |
|
| LIG_RPA_C_ 1 | R[QN][RK].[AL] | PMID:11081631 PMID:19793862 PDB:1DPU | RPA recognition motif found in DNA repair proteins SMARCAL1, Tipin, UNG2, XPA and AD52 |
first draft |
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| LIG_SCF_COI1 | RR..L..FL | PMID:17637675 PMID:20927106 PDB:3OGM PMID:17637677 PMID:18458331 PMID:20159850 | a degron found in plants associated with the Jasmonate family of transcription repressors. |
first draft |
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| LIG_PAM2_2 | EF.PG..W | PMID:20098421,PDB:2X04 | Second PABC PAM2 motif that has a different path and exit on the domain face. Found in TNRC6C. Won't match current expression and therefore needs own class. | undeleted |
first draft |
|
| LIG_CP_1 | L.H.T..R[AP]K | PMID:20625546, PDB:3AA0 , PDB:3AA1 , PDB:3AA6 | Actin Capping Protein (CP)-binding motif of CARMIL proteins (CARMIL, CD2AP, CKIP-1) | undeleted |
first draft |
|
| LIG_SCF_TIR1 | GWPPV | PMIDPMID:15295098 PMID:11595806 PMID:16488128 PMID:17410169 PDB:2P1Q | A degron motif found in plants responsible for the degradation of members of the Aux/IAA family of transcriptional repressors |
first draft |
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| LIG_TKB | (Y)[TS]..PT | PMID:20877636, PMID:18273061, PDB:3OB1 , PDB:3OB2 | Recognition motif in EGFR and Sprouty2 for non-canonical SH2 domain (TKB domain) in E3 ubiquitin ligase c-Cbl |
first draft |
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| CLV_C14_Caspase4-5 | [LIVMWYF][EDQ][^RKGL]D | PMID:1221285 PMID: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 |
|
| CLV_C14_Caspase-2 | [DEIL].[DEFY]D | PMID:1221285 PMID:1236692 PMID: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 |
|
| CLV_C14_Caspase-9 | [^RK][EDQ]HD | PMID:1221285 PMID:1236692 PMID: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 |
|
| CLV_C14_Caspase-8-10 | [^RK][EDQ].D | PMID:1221285 PMID:1236692 PMID:19694615 PMID:10964557 PMID: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. |
first draft |
|
| CLV_C14_Caspase-6 | VLIT][EDQ][^DENQRKAPGS]D | PMID:1221285 PMID:1236692 PMID:19694615 PMID: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 |
|
| LIG_TPR_Kinesin_1 | [ILMV].WD[DN][ES] | PMID:16760430 PMID:20195521 | Motif in calsyntenin binding to TPR (tetratricopeptide repeat) domains of Kinesin Light Chain1 (KLC1. Also used by Vaccinia Virus. |
first draft |
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| 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 |
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| LIG_RIP_CTP | SD[DE]DMGFGLFD$ | PMID:19073700 PDB: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 |
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| LIG_PUL_PLAA_1 | [DE][DE][DE][DE]LY[AGS]$ | PDB:3EBB PMID: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 |
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| LIG_Glycolytic_Aldolase | W[DE]{2,3}W | PDB:3LGE PMID:20129922 | Motif that mediates binding to Aldolase A |
first draft |
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| LIG_SH3_9 | SAMP | PMID:18786926 PMID:20509626 PDB:2RQU | a non-canonical SH3 binding motif associated binding to ASAP1 and colocalized at microtubule ends. |
first draft |
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| LIG_SH3_8 | [RK]..[RK] | PMID:12176364 PDB:1H3H PMID:15483625 | non canonical SH3 binding motif |
first draft |
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| LIG_Alpha-synuclein | .DVF. | PMID:19762560 | interaction with coiled coils of Synphilin-1 |
first draft |
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| LIG_GABARAP | W.FL | PMID:19154346 PMID:18027972 PMID:17916189 PDB:3DOW | GABAA receptor binding to clathrin and calreticulin. possibly linked to trafficking |
first draft |
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| LIG_AP_GAE_2 | W..[FW] | PMID:14973137 | 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 |
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| LIG_Actin_DMD | LK..E[ST] | PMID:9883911 | actin binding motif found in the Dp71 dystrophin isoform |
first draft |
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| LIG_ECD_CRF | LM..I$ | PMID:18801728, PDB:3EHT | Extracellular domain (ECD) of corticotropin-releasing factor (CRF) receptor 1 (CRFR1) binds to CRF via its C terminally amidated ligand motif. |
first draft |
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| LIG_BTB_SMRT | [GL][IV][AT]T[IV]KE[AM]GRSIHEIPR | PMID:14690607, PDB:1R2B | Motif mediating binding of BCL6 BTB domain to SMRT |
first draft |
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| LIG_MYND_2 | PPPLI | PMID:17560331, PDB: 2ODD | Motif that mediates the interaction between MYND domain of AML1/ETO and co-repressors SMRT and N-CoR. |
first draft |
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| LIG_EAR | PMID:20935498 PMID:11487705 | EAR motif mediates transcriptional repression of plant genes via recruitment of a histone deacetylase complex, which leads to chromatin modification. |
first draft |
|||
| LIG_CP | L.H.T..R[AP]K | PMID:20625546, PDB:3AA6 , PDB:3AA1 , PDB: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. |
first draft |
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| LIG_WD40_WDR5_1 | PMID:16829960 | Motif around K4 in H3 tail that binds to WD40 domain in WDR5 but - against expectation - does not mind if K4 is methylated. |
first draft |
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| LIG_CEP55 | GPP...Y | PMID:18948538, PDB:3E1R | motif in Alix and TSG101 that interacts with coiled coil in CEP55; motif overlaps with motif for binding to ALG-2 |
first draft |
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| TRG_Golgi | PMID:21283809 | potential Golgi-retention motif and a number of conserved motifs with unknown function |
first draft |
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| LIG_SH3_7 | [RK][RK].PXXPPXXP..[RK] | PMID: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 |
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| LIG_SH3_6 | [RK][RK].{9}[RK][RK].PXXPXX[RK]...[RK] | PMID: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 |
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| MOD_acetyl_E2ligase_1 | [KR]R[IL].KE | PMID:21791702 | Motif found associated with the acetylation of ubiquitin E2 ligases |
first draft |
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| LIG_ARM | [DEG].EGGGE.D...[FY]....L | PMID:20371349, PDB:3L6Y | Motif in JMD domain in C-terminal tail of cadherins that interacts with Armadillo repeats in p120 catenin |
first draft |
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| LIG_PAM2_2 | W..EF.PG..W.... | PMID:20098421, PMID:20181956, PDB:2X04 , PDB:3KTP | binding motif in GW182 family proteins for binding with PABC domain of PABP1, essential for microRNA-mediated translation repression and deadenylation |
first draft |
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| LIG_BH1_BH3 | LA..GD | PMID:16475813 | Motif of Bid-BH3 that binds to BH1 domain of Bcl-w. This interaction is lost upon Bcl-w lipid binding |
first draft |
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| LIG_Filamin | ..(T)TT.. | PMID:20332112, PMID:18550856, PDB: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 |
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| LIG_Talin | [WY].{4}NP.Y | PMID:15362227, PMID:20332112, PMID:19903453, PMID: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 |
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| LIG_Sin3_4 | [FLW]..[ILV][ILV]... | PMID:21440557, PDB: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 |
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| LIG_TF2_FCP1_1 | [DE]...[ILMV][AGS]..L..[DE][ILMF] | PMID:12732728, PMID:12591941, PDB: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 |
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| LIG_CAVB_AID | L.GY..WI | PMID:15141227, PDB: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 |
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| LIG_FERM_4 | MDW.....[LI]F..[LF] | PMID:16615918,PDB: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 |
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| LIG_FERM_3 | [KRQ]...Y..[ILV] | PMID:12554651,PMID:18076570, PMID:18753140, PDB:2YVC , PDB:2EMS , PDB:2ZPY , PDB: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 |
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| LIG_FERM_2 | L...M..L..LM..L..IT | PMID:21642953, PMID:21321230, PDB:3PZD | Large cargo recognition helix in DCC, Ngn and Fz1A that binds to the FERM domain of Myosin-X. |
first draft |
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| LIG_20S | [ILMV]Y.$ | PMID:21499243, PMID:20019667, PDB: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 |
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| LIG_PH_Tfb1 | [ILVF]..W[ILVF].[DE] | PMID:16793543,PDB: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). |
first draft |
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| LIG_CORNRBOX_2 | [IL]..[ILV][IL]..[ILVYF] | PMID:20581824,PDB: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 |
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| LIG_RCT | L..L[KR].[KR] | PMID:21217703,PDB: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 |
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| LIG_Caveolin | [WFY]....[WFY]..[WFY] | PMID: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 |
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| MOD_phos_NEK2 | [FLM][^P][^P]([ST])[^DEP][HR] | PMID:21712545 | Canonical motif phosphorylated by NEK2 |
first draft |
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| MOD_phos_AURORA | R.([ST]) | PMID:21712546, PMID:21712545 | Canonical motif phosphorylated by Aurora kinase A/B |
first draft |
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| LIG_APH1 | G...G | PMID:18061918, PMID: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 |
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| LIG_AcetylCoA | [QR]..G.[GA] | PMID: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 |
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| MOD_HEME | CP[ILMVFY] | PMID:7835342 | Short sequence that has been shown to bind heme and is repeated up to 6 times. |
first draft |
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| DCK_dephos_PP1_4 | F..[KR].[KR] | PMID:12115603, PMID:20376316 | Docking motif for PP1 phosphatase found in several proteins involved in apoptosis such as Bcl-xL. |
first draft |
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| DCK_dephos_PP1_3 | [GS]IL[RK] | PMID:12657641 | Docking motif, referred to as the SILK motif, for PP1 phosphatase found in NIPP1 |
first draft |
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| DCK_dephos_PP1_2 | R..Q[VIL][KR].[YW] | PMID:15164081 | Docking motif, referred to as the MyPhoNe motif, for PP1 phosphatase found in Myosin phosphatase-targeting subunit 1. |
first draft |
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| MOD_SPalmitoyl_X | PMID: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 |
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| LIG_FERM_ICAM2 | R...Y.V...W | PMID:12554651, PDB: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 |
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| LIG_HBOX_DDB1 | PMID: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 |
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| LIG_cpSR43_ANK | DPLG | PMID:18621669, PDB:3DEP | The DPLG motif binds L18p to cpSRP43. Part of a chloroplast system inserting light harvesting proteins into thylakoid membranes |
first draft |
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| LIG_Cdc20_Spo13 | L.E...N | PMID:17493939 | Degron in the yeast meiosis-specific protein SPO13 recognised by the cdc20 subunit of the APC. |
first draft |
||
| MOD_SMAD | (S)[IVLM](S)$ | PMID:9346908, PMID:18387785 | C-terminal phosphorylation motif found in receptor-activated Smads. Phosphorylated by TGF-beta1 kinase after its activation |
first draft |
||
| CLV_Separin | S[HILMV][DE].GR[RKS] | PMID:11533655 | Recognition site for cleavage by Caspase-like protease Separin. |
first draft |
||
| LIG_DHB_DAXX | [DE]..[IL]..[WHFY][[WFHY] | PMID: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 |
|
| LIG_N_degron_Doa10_Ac | ^([MAVSTC]) | PMID:20110468 | Acetylated N-terminal degron signal recognized by ubiquitin ligase Doa10. Promotes proteosomal degradation. |
first draft |
||
| LIG_PP2B_2 | L.VP | PMID:19285944 | Secondary, lower affinity, docking motif for the calcium activated phosphotase calcineurin. Found in NFAT1-4, KSR2 and Rcn1. |
first draft |
||
| LIG_Menin_MBM_2 | PMID:20961854 | 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. |
first draft |
|||
| LIG_Menin_MBM_1 | ...WRFP..P | PMID:20961854 | 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. | May not be a motif as we currently define them as it is quite a large interaction interface. |
first draft |
|
| LIG_Pex3P_1 | L..LL...L..F | PMID:21102411 | Large induced hydrophobic helix mediating binding to the Pex3p protein, found in Pex19p. |
first draft |
||
| LIG_AGO_PIWI_1 | WG | PMID: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 |
|
| LIG_BIR_Survivin | ^AX(PT) | PMID: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 |
||
| MOD_methylation | PMID:8366133 | Modification sites in histone tails and nucleolin. |
first draft |
|||
| MOD_MegPhos | PPPSP | PMID:17555532 | Necessary for phosphorylation of Megalin, possibly by GSK3. |
first draft |
||
| MOD_LammerK | (RS)n | PMID:11827553, PMID:1577277, PMID:8772383 | Many Lammer kinases (clk1-4, Doa, PK12) phosphorylate (RS)n motifs, regulating splicing. |
first draft |
||
| MOD_acetylation | PMID:10656693, PMID:10607594, PMID:9744860, PMID:9774110, PMID:9809067 | Acetylation targets in the nucleus beyond histone tails: p53, HMG I/Y, TCF, etc. |
first draft |
|||
| LIG_TRADD | YYD$ | PMID:9356494 | Tumor necrosis factor receptor-associated death domain protein (TRADD) binding motif in LMP1 |
first draft |
||
| LIG_Sap1_Bbox | F.L..L | PMID:11406578 | SRF binding motif with beta-augmentation core. |
first draft |
||
| LIG_R3IM | [DE][DE][DE]EFE[DE] | PMID:18775730 | Motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. |
first draft |
||
| LIG_RHIM_1 | [IV]Q[ILV]G | PMID:20346680 | RIP homotypic interaction motif found in several programmed necrotic cell injury related proteins. Probably the core of a longer disordered interface |
first draft |
||
| LIG_PKC | [YF][SA][VI](Y)[QR].[YF]. | PMID:15851033 | Phosphotyrosine motif in CDCP1 binding to the PKCd C2 domain. |
first draft |
||
| LIG_PHDfingers_H3 | ^...K | PMID:16728977 | NURF and ING types of PHD finger bind histone H3 trimethylated lysine. |
first draft |
||
| LIG_PAS_STAT6 | L..LL | PMID:14757047, PMID:12138096 | Stat6 motif found in complex wit the PAS domain of NCoA, not the usual nuclear receptor. Indicates a more complex story. |
first draft |
||
| LIG_PAM2 | [FPLV][^P][IPVTA].A..F.P | PMID:14685257, PMID:15003521, PMID:20096703 | PABC/MLLE2-binding motifs involved in translational regulation. |
first draft |
||
| Lig_PAH1_SID | PMID:16288918, PMID: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 |
|||
| LIG_PABC | PMID:14685257, PDB:1JH4 | Long disordered motif making many contacts??? PAM1 motif, binds to PABC domain |
first draft |
|||
| LIG_RNA_RGG | RGG | PMID:8290338, PMID:12925994, PMID:12628254 | Motif potentially involved in RNA binding in RGG transcriptional regulators. SMN Tudor domain binds dimethyl-Arg of RGG. |
first draft |
||
| LIG_Notch | DSL | PMID:17006545 | Conserved N-terminal motif in Notch ligands. |
first draft |
||
| LIG_MYPT1 | Y.Y | PMID:15164081 | 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 |
||
| TRG_PEXEL_VTS | PMID:16046186 | Export motif for RBC stage of the malaria parasite. Similar motif in potato blight. |
first draft |
|||
| TRG_Parasite_HT | R.L.[EDQ] | PMID:18621946, PMID: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 |
||
| TRG_TAT | [ST]RR.FLK | PMID:16987314 | Tat export consensus motif. |
first draft |
||
| TRG_RS | (RS)n | PMID:12215544, PMID:1577277, PMID: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 |
||
| LIG_MIT_MIM2 | [ILMV]P[DE]VP[ST]..LP | PMID:18606141, PDB:2K3W | VPS4 MIT domain binding "MIM2? motif found in a subset of ESCRT-III subunits |
first draft |
||
| LIG_TAZ1 | LP.L / LPMSP | PMID:14594809, PMID:12778114, PMID:11959977, PDB:1L8C , PDB: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 |
||
| TRG_Paranodin | PGY | PMID:17093057 | Paranodin trafficking repeat motif. |
first draft |
||
| TRG_TGN | YW | PMID:16978406 | Retrograde endosome to trans-Golgi network motif. |
first draft |
||
| TRG_VTS | R.L.[EQ] | PMID:15591203, PMID:15591202 | Vacuolar protein export signal. |
first draft |
||
| TRG_nucleolus | PMID:10469277, PMID:10050887, PMID:9731210 | Nucleolar targeting signals. |
first draft |
|||
| TRG_Mit | PMID:11381593 | Mitochondrial targetting peptides. |
first draft |
|||
| TRG_ERM-PM | RGGKYSV | PMID:17995939 | Motif responsible for the recruitment of ERM proteins to the plasma membrane in neurogenesis. |
first draft |
||
| TRG_Dendritic | LLY..[FYW] | PMID:16988049 | Dendritic targeting motif. |
first draft |
||
| TRG_chloroplast | PMID:10998602 | Chloroplast transit peptides. |
first draft |
|||
| MOD_Prk1p_1 | [LVIM]....(T)G | PMID:13679512, PMID:11694597, PMID: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 |
||
| MOD_neddylation | PMID:15361859 | Motif in UBC12 (Neddylation E2) that binds in a groove of UBA3 in the E1 complex determining a neddylation specific interaction. |
first draft |
|||
| FUN_GPIanchor | PMID:11814051, PMID:11677780, PMID:7482705 | Glycosylphosphatidylinositol extracellular plasma membrane anchor. |
first draft |
|||
| FUN_Oxidative_stress | D.ETGE | PMID:16507366, PMID:16888629 | Oxidative stress response motif in Nrf2 binding to Keap1 beta propeller domain. A second Nrf2 motif LxxQDxDLG may bind the same site. |
first draft |
||
| LIG_Chromatin_H2A-H2B | M.LRSG | PMID:18688256, PMID: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 |
||
| LIG_CKB_1 | M.E.L.LC(ST)G.F | PMID:15707391, PMID:12545175 | Triple phosphorylated docking motif in Claspin that binds checkpoint kinase CHK1 |
first draft |
||
| LIG_KLC1 | [ILMV].WD.. | PMID:16760430 | motif mediating binding to the tetratricopeptide repeats of KLC1 |
first draft |
||
| LIG_MIT_MIM1 | [DE]..L..RL..L[KR] | PMID:17928861, PDB:2V6Y | VPS4 MIT domain binding "MIM1? motif found in a subset of ESCRT-III subunits |
first draft |
||
| LIG_integrin_extracell | LDV | PMID:19255442 | Another extracellular integrin binding motif. |
first draft |
||
| LG_CyclophinA | FGP.LP | PMID:15845542 | Motif proposed to bind Cyclophin A. |
first draft |
||
| FUN_RANK | P[VILF]QE | PMID:16260781 | Cytoplasmic RANK motif mediating osteoclast formation, survival and function. |
first draft |
||
| LIG_epitope | MYPPPY | PMID: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 |
||
| LIG_CtBP_2 | RRT..PPAL | PMID:12805226 | Another motif that binds to CtBP. |
first draft |
||
| LIG_MDAS_MEF2 | PMID: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 |
|||
| LIG_LOK | [KR]Y.[ST] | PMID:16616188 | LOK kinase optimal phosphorylation site. LOK is a basophilic kinase with unusual Y preference at position 2. |
first draft |
||
| LIG_LIM | [IVLMF]I[IVLMF]R[IVLMF] | PMID: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 |
||
| LIG_FF | PMID:12381297, PMID:16253993 | Phosphorylated and possibly other motifs bind FF domains. Notably the RNA polII CTD. |
first draft |
|||
| LIG_FERM | RSLE | PMID:17045809 | A FERM domain binding motif in neurofascin. |
first draft |
||
| LIG_FAT_Reverse | L..L[LM] | PMID:18078954,PDB: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. |
first draft |
||
| LIG_ERCC1 | D[ST]G[AG]GF | PMID:17948053 | Used by XPA to recruits ERCC1-XPF to nucleotide excision repair complexes |
first draft |
||
| LIG_CSL | [VILMF]W[VILMF]P | PMID:15297877 | N-terminal motif in Notch, responsible for its interaction with the CSL transcription factor in the nucleus to activate the pathway. |
first draft |
||
| LIG_COPII | YNNSNPF, L..LE , D.E | PMID:12941276, PMID:15093828 | Motifs involved in vesicle budding interactions of SNARES with COPII (subunits sec23/24). |
first draft |
||
| LIG_AIM | [WY]..[ILV] | PMID:20083108,PDB:3dow ,PDB:2zzp ,PDB:2zjd ,PDB:2zpn | Atg8-family interacting motif (AIM) found in Atg19, p62, Atg4B and Calreticulin, involved in autophagy related processes |
first draft |
||
| CLV_GxGD | G.GD | PMID:20021564 | Motif that could be evolutionary conserved to allow cleavage of all possible gamma-secretase substrates. |
first draft |
||
| FAM_apoptotic | XX...DD....D | Motif found in apoptosis induction proteins: GPP synthases, Nox-a, Bad, Bid, Bik, yt-ppy-a, s81f. |
first draft |
|||
| FAM_nucleus_transcription | R..PY..P | PMID:15703190 | Conserved in some TBOX, ATF4/5 and some hnRNP proteins. Reported as nuclear localisation signal but the point mutants are not consistent. |
first draft |
||
| FUN_Aurora | PMID:14752279 | Double motif in TPX2 regulating Aurora kinase activity |
first draft |
|||
| LIG_clathr_ClatBox_Cter | L[IVLMF].[IVLMF]$ | PMID:10449404 | Variant clathrin box in yeast found at carboxy termini of e.g. some epsins. |
first draft |
||
| LIG_CK1 | F...F | PMID:15121840 | Motif in NFAT and Per reported to dock CK1 kinase. Reminiscent of the FXXF motif in the PIF pocket kinases. |
first draft |
||
| LIG_CH_Parvin_Backwards | L..L[LM]..LE | PMID:18940607, PDB: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 |
||
| LIG_CH_Parvin_Forwards | EL..L[LM]..L | PMID:18940607, PDB: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 |
||
| LIG_chromoshadow_EMSY | [VILMF].[VILMF].[VILMF]..[VILMF] | PMID:16615912 | Motif that binds to HP1 chromoshadow domains from EMSY. |
first draft |
||
| LIG_Calnexin | KPKKKKK | PMID: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 |
||
| LIG_betaCatenin_armadillo | PMID:11136974, PMID: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 |
|||
| LIG_AP2alpha_3 | W..[FW] | PMID:14565955 | An AP-2 adaptor interaction motif initially identified in the long-splice isoform of Synaptojanin1. |
first draft |
||
| LIG_AnkyrinG | [VA]P[IL]A..E[SD]D | PMID:12716895, PMID:12829783 | A conserved 9-amino acid motif required for ankyrinG binding. |
first draft |
||
| LIG_alphaActin | FGPVVA | PMID:1142354 | Actin binding motif in plaque protein zyxin. Said to require alpha-actinin dimerisation. |
first draft |
||
| LIG_Abox | PMID:12208850 | Another destruction box proposed in Aurora A kinases. |
first draft |
|||
| FUN_UBX | QA | PMID:16267091 | Motif is present in Drosophila Ubx family of HOX genes and with pleiotropic functions in development. |
first draft |
||
| FUN_Synaptotagmin | KK...K | PMID:16987956 | Motif required for efficient synaptic transmission. |
first draft |
||
| FUN_Pin1_Isomerisation | P[ST]P | PMID:12571275 | Pin1 isomerization motif. |
first draft |
||
| FUN_N-end_rule_pathway | PMID:17962019 | N-terminal ubiquitin mediated destruction system. May be ancient. Might not be a single motif but a combination of post translational modifications. |
first draft |
|||
| FUN_FG_nucleoporin | (FG)n | PMID:18688269 | 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 |
||
| FUN_Delta | [DE].{2,4}NN[IL] | PMID: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 |
||
| LIG_Fn_binding | LIPAD | PMID: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 |
||
| LIG_integrin_TGFbeta | DL..L | PMID:14572313 | Integrin binding motif in TGFbeta. |
first draft |
||
| LIG_Integrin_Cell_Adhesion | GRKRK | PMID: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 |
||
| LIG_IntA3B1 | NVR | PMID:17034138 | Integrin a3b1 binding motif in thrombospondin. |
first draft |
||
| LIG_Hsc70 | QLMLT | PMID:17978091, PMID: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 |
||
| LIG_RhoGAP_OCRL_1 | F...H..[ILVFY] | PDB:PMID :21666675,PDB:3QIS | F&H motif mediates binding to the RhoGAP domain of OCRL. Found in Ses1, Ses2 and APPL1. |
undergoing annotation |
||
| LIG_ALG2 | PPYP.{1,4}YP | PMID:18940611, PDB: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 |
undergoing annotation |
||
| LIG_SUMO_SBM | V.[VI][VI] | PMID:15388847, PMID:16524884, PMID:19812159 | Motif reported to bind SUMO present in RanBP2, PML, among cothers. |
undergoing annotation |
||
| LIG_SPRY_SPSB | [DE][IL]NNN | PMID:20561531, PDB: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 |
undergoing annotation |
||
| LIG_Wnt | LT...W | PMID:10990458 | 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. |
undergoing annotation |
||
| MOD_HedgehogLipid | PMID:9593755, PMID:11486055, PMID:11493554 | Keeps Hedgehog attached to plasma membrane for short range extracellular signalling. Probably needs its own functional site and different ELM entries. |
undergoing annotation |
|||
| DCK_phos_PKA_1 | [ILMVFA][ILMVFA]..[ILMVFA]...[ILMVFA][ILMVFA]..[ILMVFA] | PMID:2015946, PDB: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 |
||
| LIG_N_degron_UBR_tertiary | ^[NQ] | PMID:17962019 | 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. |
undergoing annotation |
||
| LIG_N_degron_UBR_secondary | ^[DEC] | PMID:17962019 | 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 |
undergoing annotation |
||
| LIG_N_degron_UBR_type2 | ^[FLWYI] | PMID:17962019 | 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. |
undergoing annotation |
||
| LIG_N_degron_UBR_type1 | ^[RKH][^P] | PMID:20835242, PMID:20835240, PDB:3NY1 , PDB: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. |
undergoing annotation |
||
| LIG_WW_Itch | PP.Y....[ST][ILV] | PMID: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 |
||
| LIG_WW_Fe65 | PPLA | PMID: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 |
|
| LIG_PLK | ..S([ST])P.. | PMID:12595692, PMID:14532005 | Phosphoserine site recognised by the Polo-like-kinase. |
undergoing annotation |
||
| LIG_Centrin_XPC | W..L...[IL] | PMID:15964821 | Motif responsible for the binding of XPC repair protein to Centrin 2. PDB structures available. |
undergoing annotation |
||
| LIG_GDB_WASP_1 | [ILV][ILVA]..LM..[ILMV] | PMID:18650806, PMID:18650809, PDB: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. |
proofreading |
||
| Lig_CAP-Gly_2 | W[KR][ED]GCY$ | PMID:21646404,PDB: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 |
|
| CLV_Caspase3-7 | D..D[AGS] | PMID:12107159 | Caspase-3/Caspase-7 cleavage motif. |
fully annotated |
||
| LIG_PIKK_1 | [DEN][DEN].{2,3}[ILMVA][DEN][DEN]L.{0,20}$ | PMID:15758953 | Docking motif for PIKK kinases family found in DNA damage proteins Nbs1, ATRIP and XRCC5. | alias DCK_phos_PIKK_1 |
fully annotated |
|
| LIG_SCF_Cks1_1 | .E.(T)P. | PMID:16209941, PDB:2AST | Phosphodegron in P27kip1 which must be targeted for destruction by SCF ubiquitination to allow the cell cycle progression |
fully annotated |
||
| LIG_SCF_SKP2 | PMID:16209941 | Complex phosphopeptide motif binding to the assembled dimer of Skp2 and Cks1 (SCF components), in the ubiquitin degradation process. |
fully annotated |
|||
| LIG_HCF-1 | [ED]H.Y | PMID:14532282 | HCF-binding motif, to bind to a six-bladed β-propeller domain at the N terminus of HCF-1 |
fully annotated |
||
| LIG_RB_pocket | [IL]..L[YF] | PMID:17974914, PMID:12598654 | Binding to the E2f binding pocket between the Rb-A and Rb-B domains |
fully annotated |
||
| LIG_SPAK-OSR1 | RF.V | PMID:17721439 | Docking motif in substrates of OSR1 and SPAK kinases that binds to the CCT domain. |
fully annotated |
||
| LIG_Integrin_isoDGR | NGR | PMID:18480047 | 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 |
||
| LIG_eIF4E_2 | Y.PP.[ILMV]R | PMID:17667941 | Mediates binding to the dorsal surface of eIF4E. Found in DDX3, eIF-3G and eIF-2A |
fully annotated |
||
| LIG_eIF4E_1 | Y....L[VILMF] | PMID:16739988 | Motif present in some interacting partners of eIF4E. |
fully annotated |
||
| LIG_Actin_WH2_1 | [ILMV][ILMV]..I.{4,7}L[KR][KR][ILMVT] | PMID:11911886,PDB:2A3Z ,PDB:2A40 ,PDB:2A41 ,PDB:2D1K ,PDB:2VCP ,PDB:3MN5 ,PDB: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 |
||
| LIG_Actin_RPEL_1 | L..[KR][IL]..R[PQ]...[ED]L..[RK].[ILMV][ILMV] | PMID:19008859,PDB: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 |
||
| LIG_PIF | F..F or F..F([ST]) | PMID:15003271 | 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 |
||
| TRG_ER-exit | LLV | PMID: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 |
[updated] |
| FAM_TypeIII | W...E | PMID: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 |
|
| LIG_HIV1-GP41 | H..NPF | PMID:16904109 | HIV-1 gp41 core-binding motif. |
deleted |
||
| CLV_C14_Caspase-8-10 | [^RK][EDQ].D | PMID:1221285 PMID:1236692 PMID:19694615 PMID:10964557 PMID: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 |
|
| LIG_CD40 | EQLKKSKTL | PMID:21998326 | Linear peptide in an exposed loop mediates interaction between CD40L and Mac-1 | might be too specific paper not freely accessible |
deleted |
|
| LIG_WW_Fe65 | PPLA | PMID:18547980 | Motif of GSK3beta that binds to Fe65. This interaction regulates apoptosis and phosphorylation of Tyr 216 of GSK3beta. | description updated |
deleted |
|
| LIG_PTB_splicing | [SG][IL]LG..P | PMID:16936729 | Motif essential for splicing repressor activity found in cofactors of the PTB regulatory splicing repressor (Polypyrimidine tract-binding protein). |
deleted |
Please cite: ELM - the database of eukaryotic linear motifs (PMID:22110040)