Currently 269 candidates need annotation:
| Identifier | Model | References | Description | Notes | Status | |
|---|---|---|---|---|---|---|
| TRG_NoDS | RR[IL].{1,10}[ILVF][ILVF][ILVF] |  22284675 |
Nucleolus targeting signals that results in sequestration of proteins by ncRNA |
first draft |
||
| LIG_APCC_#R_1 | .[LM]R$ | 23288039, 16648845 |
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 |
first draft |
||
| LIG_APCC_IR_1 | .IR$ | 15916960,12574115,12956947 |
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. |
first draft |
||
| 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 |
||
| 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 |
||
| 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 |
||
| LIG_sHSP_IxI_1 | .I.[IV]. | 23188086,23340341 |
Oligomerisation motif of alpha-crystallins and related small heat shock proteins. |
first draft |
||
| LIG_SH3_8 | [RK]..[RK] | 12176364 1H3H 15483625 |
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 |
|
| 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 |
|
| MOD_CDK_3 | ([ST])P... | 16244663 |
variant motif; instance does not match current RegEx | instance in switches.elm: SWTI000284 MK67I_HUMAN (Q9BYG3) 235 241 |
first draft |
|
| 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 |
|
| LIG_Dynein_DLC8_2 | [KR].TMT | 17029413;16981716 |
variant | instance in switches.elm: SWTI000541 MYO5A_HUMAN (Q9Y4I1) 1286 1290 |
first draft |
|
| CLV_CASPASE3_1 | D..D | 12637508 |
relaxed Caspase3-1 cleavage site | instance in switches.elm: SWTI000550 CEAM1_MOUSE (P31809) 457 460 |
first draft |
|
| 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 |
||
| 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 |
|
| TRG_NES | 18715118 |
NES |
first draft |
|||
| LIG_BROMO_BET | (K)[GILVMF]{0,1}[^MFYLW].(K) | 2WP2 1979449522464331 |
Diacetylation recgnition motif for bromodomain of BET family | first BRDs of the BET family |
first draft |
|
| LIG_BROMO | 20502673,11080160 1E6I |
The Bromodomain binds acetylated lysine residues in the flexible N- and C-terminal tails of histones. |
first draft |
|||
| LIG_SCF-TrCP1_2 | [EDST][ESTD][GAS].{1,3}[STD] | 1915043214676825150707331584577118354483173871461837867015917222157676832004800120858893 |
non-canonical variants of the LIG_SCF-TrCP1_1 |
first draft |
||
| TRG_NLS | 12244301 1594241 9885291 21092142 21182795 |
non-canonical nuclear localisation signals |
first draft |
|||
| 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 |
|
| Mod_PLK_1 | (.[DEN][^GP]([ST])[FILMVW]..) or (.[DEN][^GP]([ST])[^P][FILMVW].) | 21712545 |
Revised PLK1 phosphosite based on peptide data. | Better description than the current ELM model. |
first draft |
|
| LIG_TPR_Kinesin_1 | [ILMV].W[ED][DN][ES] | 167604302019552122172677 |
Motif in calsyntenin binding to TPR (tetratricopeptide repeat) domains of Kinesin Light Chain1 (KLC1. Also used by Vaccinia Virus. |
first draft |
||
| LIG_MBT | 20502673 1OYX 12842041 |
Malignant brain tumor (MBT) repeats have been implicated as methyl-lysine binding modules. |
first draft |
|||
| LIG_CHROMO | ARK[ST] | 20502673 1KNA 11859155 |
Chromo domains promote binding to methylated lysines in Histone H3 tails. |
first draft |
||
| LIG_GLi | SYGH | 12426310 |
responsible for Gli proteins interactions with Sufu. |
first draft |
||
| LIG_SCF_TIR1 | GWPPV | 152950981159580616488128174101692P1Q |
A degron motif found in plants responsible for the degradation of members of the Aux/IAA family of transcriptional repressors |
first draft |
||
| 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. |
first draft |
||
| MOD_SUMO_PHOS | [VILMAFP](K).[ST]. | 22586270 |
Novel Sumoylation site found in Estrogen receptor beta connected to a GSK-beta phosphorylation site |
first draft |
||
| 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 |
||
| LIG_ANKRIN_ANKRA2_1 | PxLPx[IL] | 22649097,3SO8,3V2O,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). |
first draft |
||
| 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 |
|
| 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 |
||
| LIG_SH2_III | (Y)..Q | 17956856 |
Group III comprises the STAT family of SH2 domains. |
first draft |
||
| LIG_SH2_IID | (Y)... | 17956856 |
this is the generic motif for Group 2 SH2 domains. |
first draft |
||
| LIG_SH2_IIC | (Y)... | 17956856 |
this is the generic motif for Group 2 SH2 domains. |
first draft |
||
| 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 |
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| 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 |
||
| LIG_SH2_IE | (Y)[DEKNPR][DEKNPR][AFILVWY] | 17956856 |
this is the generic motif for Group 1 SH2 domains. |
first draft |
||
| LIG_SH2_ID | (Y)[DEKNPR][DEKNPR][AFILVWY] | 17956856 |
this is the generic motif for Group 1 SH2 domains. |
first draft |
||
| 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 |
||
| 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 |
||
| TRG_ER_diArg_2 | .RR. | 14527949 |
Generic di-arginine ER retention motif |
first draft |
||
| TRG_AP2beta_CARGO_2 | [FY]F.{6}W.[FY] | 19287005 |
non-canonical AP2-beta2 binding found in isoform of PIPKIγ |
first draft |
||
| TRG_NES_CRM1_2 | L.{2,3}L.L | 11074002 |
very general NES |
first draft |
||
| 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 |
|
| LIG_APCC_Dbox_3 | .R.{2,3}L.{1,3}[LIVM] | 1174298811285280 |
Extended Dbox also tends to have further residues upstream that are required for recognition |
first draft |
||
| CLV_C14_Metacaspase | 17028019,18005666,19820703,21597462 |
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 |
||
| LIG_TRAF2_3 | P.Q.[ST] | 1291769110518213105182131CZY 1QSC 1CZZ |
Slight variant of LIG_TRAF motifs already in ELM. |
first draft |
||
| TRG_LysEnd_APsAcLL_2 | [DERQ].{2,4}L[LVI] | 1831553010611976 |
Slight variation of TRG_LysEnd_APsAcLL_1 |
first draft |
||
| TRG_MLS | 221781381083724416616497 |
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] | 9141499880551081273651235184611911888 |
extended IQ motif |
first draft |
||
| LIG_IQ_2 | [FILV]Q...[RK] | 9141499880551081273651235184611911888 |
IQ-like motif. |
first draft |
||
| LIG_PCNA_2 | [ILVM][^ILVM][DHFM][ILVM] | 11682605 |
slight variation on original PCNA motif |
first draft |
||
| LIG_BIR_internal | A.[AP]. | 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] | 9891784,15483625 |
lipid binding motif for PI(4,5)P2 |
first draft |
||
| LIG_Filamin_2 | Y..A[VIL]...[VIL] | 164554892BRQ |
Based on integrin binding to filamin |
No mention of importance of threonines defined in LIG_Filamin |
first draft |
|
| LIG_TNK_1 | R..PDG | 22153076,22153077 |
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 |
||
| LIG_CYCLIN_2 | L..P[ILVMF].[ILVMF] | 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] | 214544783Q4A |
phosphorylated version of LIG_TPR found in Smad 1/5 |
first draft |
||
| LIG_TPR_3 | K[IL].{0,2}Q | 1875945717942943 |
internal TPR binding motif with similatities found in androgen receptor and vpu | unsure of veracity |
first draft |
|
| 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 |
||
| LIG_MIU | [DE][LIVY].[LIV]A..[LIVY]..[DE]{DE] | 164999582C7N 2C7M 19217402 |
MIU (motif interacting with ubiquitin; also known as IUIM or inverted UIM) |
first draft |
||
| 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 |
|
| LIG_DUIM | [DE].[LIVY]..A[LIVYM]A.S.[SA][DE] | 16462748
2D3G |
double sided ubiquitin interacting motif |
first draft |
||
| LIG_UIM | [DE][DE]..[ILVY]..A[ILVY].S.. | 16462748
12970172
1Q0V
2D3G
12750381
1O06 |
Ubiquitin interacting motif |
first draft |
||
| MOD_N-GLC_Bacteria | [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 |
|
| MOD_N-GLC_3 | NG. | 20510933
21978957 |
Non-canonical N-glycosylations sites found in the mouse glycoproteome |
first draft |
||
| MOD_N-GLC_4 | N.V | 20510933
21978957 |
Non-canonical N-glycosylations sites found in the mouse glycoproteome |
first draft |
||
| LIG_CASK_CID_1 | E.[IV]W[IV].R | 21763699 |
Docking motif in Caskin1, Mint1 and TIAM1 that binds to the CASK hub protein involved in brain, synapse, cell polarity. |
first draft |
||
| LIG_PCNA_PIP_2 | ...[LIM][DE].[FHY][FHY]. | 19208623, 2ZVM,20606006,19081076 |
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 | 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 |
|
| LIG_WW_Nedd4L | .(S)P.L(S)PN | 21685363, 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 |
||
| MOD_Geranyl_CAAXbox_1 | (C).[LIVM][ILMV]$ | 12702202 |
Motif modified by Geranylgeranyltransferase I (GGT1). | Should replace current MOD_CAAXbox to define specificity. |
first draft |
|
| MOD_Farnesyl_CAAXbox_1 | (C).[LIVM].$ | 12702202 |
Motif modified by Farnesyltransferase. | Should replace current MOD_CAAXbox to define specificity. |
first draft |
|
| LIG_DCUN1_1 | (M)[IL].L | 21940857
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 | 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 |
|
| LIG_RPA_C_ 1 | R[QN][RK].[AL] | 11081631
19793862
1DPU
|
RPA recognition motif found in DNA repair proteins SMARCAL1, Tipin, UNG2, XPA and AD52 |
first draft |
||
| LIG_SCF_COI1 | RR..L..FL | 17637675
20927106
3OGM
17637677
18458331
20159850 |
a degron found in plants associated with the Jasmonate family of transcription repressors. |
first draft |
||
| LIG_PAM2_2 | EF.PG..W | 20098421,2X04 |
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 | 20625546, 3AA0, 3AA1, 3AA6 |
Actin Capping Protein (CP)-binding motif of CARMIL proteins (CARMIL, CD2AP, CKIP-1) | undeleted |
first draft |
|
| 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 |
||
| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
||
| 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 |
||
| 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 |
||
| LIG_Glycolytic_Aldolase | W[DE]{2,3}W | 3LGE
20129922 |
Motif that mediates binding to Aldolase A |
first draft |
||
| LIG_SH3_9 | SAMP | 18786926
20509626
2RQU |
a non-canonical SH3 binding motif associated binding to ASAP1 and colocalized at microtubule ends. |
first draft |
||
| LIG_Alpha-synuclein | .DVF. | 19762560 |
interaction with coiled coils of Synphilin-1 |
first draft |
||
| LIG_AP_GAE_2 | W..[FW] | 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 |
||
| LIG_Actin_DMD | LK..E[ST] | 9883911 |
actin binding motif found in the Dp71 dystrophin isoform |
first draft |
||
| 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 |
||
| LIG_BTB_SMRT | [GL][IV][AT]T[IV]KE[AM]GRSIHEIPR | 14690607, 1R2B |
Motif mediating binding of BCL6 BTB domain to SMRT |
first draft |
||
| 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 |
|||
| 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. |
first draft |
||
| LIG_WD40_WDR5_1 | 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 |
|||
| LIG_CEP55 | GPP...Y | 18948538, 3E1R |
motif in Alix and TSG101 that interacts with coiled coil in CEP55; motif overlaps with motif for binding to ALG-2 |
first draft |
||
| TRG_Golgi | 21283809 |
potential Golgi-retention motif and a number of conserved motifs with unknown function |
first draft |
|||
| 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 |
||
| 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 |
||
| MOD_acetyl_E2ligase_1 | [KR]R[IL].KE | 21791702 |
Motif found associated with the acetylation of ubiquitin E2 ligases |
first draft |
||
| 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 |
||
| LIG_PAM2_2 | W..EF.PG..W.... | 20098421,20181956, 2X04, 3KTP |
binding motif in GW182 family proteins for binding with PABC domain of PABP1, essential for microRNA-mediated translation repression and deadenylation |
first draft |
||
| 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 |
||
| LIG_Filamin | ..(T)TT.. | 20332112,18550856, 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 |
|
| 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 |
||
| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
||
| 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 |
||
| 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 |
||
| 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 |
||
| 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). |
first draft |
||
| LIG_CORNRBOX_2 | [IL]..[ILV][IL]..[ILVYF] | 20581824,3N00 |
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 |
||
| 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 |
||
| 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 |
||
| MOD_phos_AURORA | R.([ST]) | 21712546,21712545 |
Canonical motif phosphorylated by Aurora kinase A/B |
first draft |
||
| 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 |
|
| 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 |
||
| MOD_HEME | CP[ILMVFY] | 7835342 |
Short sequence that has been shown to bind heme and is repeated up to 6 times. |
first draft |
||
| 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 |
||
| DCK_dephos_PP1_3 | [GS]IL[RK] | 12657641 |
Docking motif, referred to as the SILK motif, for PP1 phosphatase found in NIPP1 |
first draft |
||
| DCK_dephos_PP1_2 | R..Q[VIL][KR].[YW] | 15164081 |
Docking motif, referred to as the MyPhoNe motif, for PP1 phosphatase found in Myosin phosphatase-targeting subunit 1. |
first draft |
||
| 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 |
||
| 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 |
|
| 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 |
||
| 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 |
||
| 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 |
||
| 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 |
||
| 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 |
|
| LIG_N_degron_Doa10_Ac | ^([MAVSTC]) | 20110468 |
Acetylated N-terminal degron signal recognized by ubiquitin ligase Doa10. Promotes proteosomal degradation. |
first draft |
||
| LIG_PP2B_2 | L.VP | 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 | 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 | 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_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 |
|
| 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 |
||
| TRG_TGN | YW | 16978406 |
Retrograde endosome to trans-Golgi network motif. |
first draft |
||
| 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 |
||
| LIG_PABC | 14685257, 1JH4 |
Long disordered motif making many contacts??? PAM1 motif, binds to PABC domain |
first draft |
|||
| LIG_Notch | DSL | 17006545 |
Conserved N-terminal motif in Notch ligands. |
first draft |
||
| MOD_acetylation | 10656693,10607594,9744860,9774110,9809067 |
Acetylation targets in the nucleus beyond histone tails: p53, HMG I/Y, TCF, etc. |
first draft |
|||
| LIG_MYPT1 | Y.Y | 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 | 16046186 |
Export motif for RBC stage of the malaria parasite. Similar motif in potato blight. |
first draft |
|||
| LIG_PHDfingers_H3 | ^...K | 16728977 |
NURF and ING types of PHD finger bind histone H3 trimethylated lysine. |
first draft |
||
| LIG_TRADD | YYD$ | 9356494 |
Tumor necrosis factor receptor-associated death domain protein (TRADD) binding motif in LMP1 |
first draft |
||
| 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 |
||
| LIG_Sap1_Bbox | F.L..L | 11406578 |
SRF binding motif with beta-augmentation core. |
first draft |
||
| 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 |
||
| MOD_MegPhos | PPPSP | 17555532 |
Necessary for phosphorylation of Megalin, possibly by GSK3. |
first draft |
||
| 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 |
||
| TRG_Paranodin | PGY | 17093057 |
Paranodin trafficking repeat motif. |
first draft |
||
| TRG_nucleolus | 10469277,10050887,9731210 |
Nucleolar targeting signals. |
first draft |
|||
| TRG_Mit | 11381593 |
Mitochondrial targetting peptides. |
first draft |
|||
| TRG_ERM-PM | RGGKYSV | 17995939 |
Motif responsible for the recruitment of ERM proteins to the plasma membrane in neurogenesis. |
first draft |
||
| LIG_PKC | [YF][SA][VI](Y)[QR].[YF]. | 15851033 |
Phosphotyrosine motif in CDCP1 binding to the PKCd C2 domain. |
first draft |
||
| TRG_Dendritic | LLY..[FYW] | 16988049 |
Dendritic targeting motif. |
first draft |
||
| TRG_chloroplast | 10998602 |
Chloroplast transit peptides. |
first draft |
|||
| 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 |
||
| LIG_R3IM | [DE][DE][DE]EFE[DE] | 18775730 |
Motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. |
first draft |
||
| 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 |
||
| TRG_TAT | [ST]RR.FLK | 16987314 |
Tat export consensus motif. |
first draft |
||
| MOD_neddylation | 15361859 |
Motif in UBC12 (Neddylation E2) that binds in a groove of UBA3 in the E1 complex determining a neddylation specific interaction. |
first draft |
|||
| MOD_methylation | 8366133 |
Modification sites in histone tails and nucleolin. |
first draft |
|||
| LIG_PAM2 | [FPLV][^P][IPVTA].A..F.P | 14685257,15003521,20096703 |
PABC/MLLE2-binding motifs involved in translational regulation. |
first draft |
||
| 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 |
||
| 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 |
|||
| MOD_LammerK | (RS)n | 11827553,1577277,8772383 |
Many Lammer kinases (clk1-4, Doa, PK12) phosphorylate (RS)n motifs, regulating splicing. |
first draft |
||
| 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 |
||
| TRG_VTS | R.L.[EQ] | 15591203,15591202 |
Vacuolar protein export signal. |
first draft |
||
| 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 |
||
| 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 |
||
| LIG_IntA3B1 | NVR | 17034138 |
Integrin a3b1 binding motif in thrombospondin. |
first draft |
||
| 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 |
||
| LIG_integrin_TGFbeta | DL..L | 14572313 |
Integrin binding motif in TGFbeta. |
first draft |
||
| 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 |
||
| 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 |
||
| FUN_FG_nucleoporin | (FG)n | 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_N-end_rule_pathway | 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_Pin1_Isomerisation | P[ST]P | 12571275 |
Pin1 isomerization motif. |
first draft |
||
| FUN_Synaptotagmin | KK...K | 16987956 |
Motif required for efficient synaptic transmission. |
first draft |
||
| FUN_UBX | QA | 16267091 |
Motif is present in Drosophila Ubx family of HOX genes and with pleiotropic functions in development. |
first draft |
||
| LIG_Abox | 12208850 |
Another destruction box proposed in Aurora A kinases. |
first draft |
|||
| LIG_alphaActin | FGPVVA | 1142354 |
Actin binding motif in plaque protein zyxin. Said to require alpha-actinin dimerisation. |
first draft |
||
| LIG_AnkyrinG | [VA]P[IL]A..E[SD]D | 12716895,12829783 |
A conserved 9-amino acid motif required for ankyrinG binding. |
first draft |
||
| LIG_AP2alpha_3 | W..[FW] | 14565955 |
An AP-2 adaptor interaction motif initially identified in the long-splice isoform of Synaptojanin1. |
first draft |
||
| 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 |
|||
| 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 |
||
| LIG_chromoshadow_EMSY | [VILMF].[VILMF].[VILMF]..[VILMF] | 16615912 |
Motif that binds to HP1 chromoshadow domains from EMSY. |
first draft |
||
| 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 |
||
| 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 |
||
| 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 |
||
| LIG_clathr_ClatBox_Cter | L[IVLMF].[IVLMF]$ | 10449404 |
Variant clathrin box in yeast found at carboxy termini of e.g. some epsins. |
first draft |
||
| LIG_COPII | YNNSNPF, L..LE, D.E | 12941276,15093828 |
Motifs involved in vesicle budding interactions of SNARES with COPII (subunits sec23/24). |
first draft |
||
| LIG_CSL | [VILMF]W[VILMF]P | 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_ERCC1 | D[ST]G[AG]GF | 17948053 |
Used by XPA to recruits ERCC1-XPF to nucleotide excision repair complexes |
first draft |
||
| 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. |
first draft |
||
| LIG_FERM | RSLE | 17045809 |
A FERM domain binding motif in neurofascin. |
first draft |
||
| LIG_FF | 12381297,16253993 |
Phosphorylated and possibly other motifs bind FF domains. Notably the RNA polII CTD. |
first draft |
|||
| 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 |
||
| LIG_LOK | [KR]Y.[ST] | 16616188 |
LOK kinase optimal phosphorylation site. LOK is a basophilic kinase with unusual Y preference at position 2. |
first draft |
||
| 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 |
|||
| FUN_Oxidative_stress | D.ETGE | 16507366,16888629 |
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 | 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 |
||
| 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 |
||
| LIG_KLC1 | [ILMV].WD.. | 16760430 |
motif mediating binding to the tetratricopeptide repeats of KLC1 |
first draft |
||
| LIG_integrin_extracell | LDV | 19255442 |
Another extracellular integrin binding motif. |
first draft |
||
| LG_CyclophinA | FGP.LP | 15845542 |
Motif proposed to bind Cyclophin A. |
first draft |
||
| FUN_RANK | P[VILF]QE | 16260781 |
Cytoplasmic RANK motif mediating osteoclast formation, survival and function. |
first draft |
||
| 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 |
||
| LIG_CtBP_2 | RRT..PPAL | 12805226 |
Another motif that binds to CtBP. |
first draft |
||
| CLV_GxGD | G.GD | 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 | 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 | 14752279 |
Double motif in TPX2 regulating Aurora kinase activity |
first draft |
|||
| FUN_GPIanchor | 11814051,11677780,7482705 |
Glycosylphosphatidylinositol extracellular plasma membrane anchor. |
first draft |
|||
| LIG_MYND_PHD2_1 | P.LE | 23413029 |
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 |
undergoing annotation |
[updated] |
| LIG_MYND_2 | PPPLI | 17560331, 2ODD |
Motif that mediates the interaction between MYND domain of AML1/ETO and co-repressors SMRT and N-CoR. |
undergoing annotation |
[updated] |
|
| 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 |
||
| Mod_CDK_Long_2 | ...[SP]..K | 21712545 |
Longer version of the cyclin/CDK phosphosite recognised by e.g. CDK1. Lysine is specific in the charge position. |
undergoing annotation |
||
| MOD_phos_NEK2 | [FLM][^P][^P]([ST])[^DEP][HR] | 21712545 |
Canonical motif phosphorylated by NEK2 |
undergoing annotation |
||
| LIG_GABARAP | W.FL | 1915434618027972179161893DOW |
GABAA receptor binding to clathrin and calreticulin. possibly linked to trafficking |
undergoing annotation |
||
| LIG_LIR | WxxL or [WYF]xx[LIV] | 21620860 |
LC3-interacting region (LIR) might link ubiquitinated substrates that should be degraded to the autophagy modifiers in the autophagosome membrane |
undergoing annotation |
||
| LIG_AIM | [WY]..[ILV] | 20083108,3dow,2zzp,2zjd,2zpn |
Atg8-family interacting motif (AIM) found in Atg19, p62, Atg4B and Calreticulin, involved in autophagy related processes |
undergoing annotation |
||
| LIG_ALG2 | PPYP.{1,4}YP | 18940611, 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_Wnt | LT...W | 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 | 9593755,11486055,11493554 |
Keeps Hedgehog attached to plasma membrane for short range extracellular signalling. Probably needs its own functional site and different ELM entries. |
undergoing annotation |
|||
| LIG_N_degron_UBR_tertiary | ^[NQ] | 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] | 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] | 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] | 20835242,20835240, 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. |
undergoing annotation |
||
| 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 |
||
| 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 |
|
| LIG_PLK | ..S([ST])P.. | 12595692,14532005 |
Phosphoserine site recognised by the Polo-like-kinase. |
undergoing annotation |
||
| LIG_Centrin_XPC | W..L...[IL] | 15964821 |
Motif responsible for the binding of XPC repair protein to Centrin 2. PDB structures available. |
undergoing annotation |
||
| LIG_GBD_WASP_1 | [ILV][ILVA]..LM..[ILMV] | 18650806, 18650809,2K42 |
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 |
||
| TRG_ER_diArg_1 | R.{0, 1}R | 16065065 |
ER retention/retrieving signal found in ER membrane proteins (cytoplasmic side) | should replace current TRG_ER_diArg_1 |
fully annotated |
|
| LIG_SCF_SKP2 | 16209941 |
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 |
||
| LIG_SPRY_SPSB | [DE][IL]NNN | 20561531, 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 | annotated as LIG_SPRY_1 |
fully annotated |
|
| LIG_PIKK_1 | [DEN][DEN].{2,3}[ILMVA][DEN][DEN]L.{0,20}$ | 15758953 |
Docking motif for PIKK kinases family found in DNA damage proteins Nbs1, ATRIP and XRCC5. | alias DCK_phos_PIKK_1 |
fully annotated |
|
| LIG_eIF4E_1 | Y....L[VILMF] | 16739988 |
Motif present in some interacting partners of eIF4E. | annotated as LIG_eIF4E_1 |
fully annotated |
|
| LIG_eIF4E_2 | Y.PP.[ILMV]R | 17667941 |
Mediates binding to the dorsal surface of eIF4E. Found in DDX3, eIF-3G and eIF-2A | annotated as LIG_eIF4E_2 |
fully annotated |
|
| MOD_LATS_1 | H.R..[ST] | 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. | annotated as MOD_LATS_1 |
fully annotated |
|
| LIG_SUMO_SBM | V.[VI][VI] | 15388847, 16524884, 19812159 |
Motif reported to bind SUMO present in RanBP2, PML, among cothers. | annotated as LIG_SUMO_SBM_1 and LIG_SUMO_SBM_2 |
fully annotated |
|
| CLV_Separin | S[HILMV][DE].GR[RKS] | 11533655 |
Recognition site for cleavage by Caspase-like protease Separin. | annotated as CLV_Separin_Metazoa and CLV_Separin_Fungi |
fully annotated |
|
| LIG_RhoGAP_OCRL_1 | F...H..[ILVFY] | PDB:21666675,3QIS |
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 |
|
| LIG_Pex3P_1 | L..LL...L..F | 21102411 |
Large induced hydrophobic helix mediating binding to the Pex3p protein, found in Pex19p. | annotated as TRG_PEX_3 |
fully annotated |
|
| Lig_CAP-Gly_2 | W[KR][ED]GCY$ | 21646404,3RDV |
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] | 12107159 |
Caspase-3/Caspase-7 cleavage motif. |
fully annotated |
||
| LIG_SCF_Cks1_1 | .E.(T)P. | 16209941, 2AST |
Phosphodegron in P27kip1 which must be targeted for destruction by SCF ubiquitination to allow the cell cycle progression |
fully annotated |
||
| LIG_HCF-1 | [ED]H.Y | 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] | 17974914,12598654 |
Binding to the E2f binding pocket between the Rb-A and Rb-B domains |
fully annotated |
||
| LIG_SPAK-OSR1 | RF.V | 17721439 |
Docking motif in substrates of OSR1 and SPAK kinases that binds to the CCT domain. |
fully annotated |
||
| LIG_Integrin_isoDGR | NGR | 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_Actin_WH2_1 | [ILMV][ILMV]..I.{4,7}L[KR][KR][ILMVT] | 11911886,2A3Z,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 |
||
| LIG_Actin_RPEL_1 | L..[KR][IL]..R[PQ]...[ED]L..[RK].[ILMV][ILMV] | 19008859,2V52 |
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]) | 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 | 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 |
|
| 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 |
|
| 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 |
|
| LIG_BCL2 | L..I[AG]D.[ILV] | 20502673 1BXL 9020082 |
Bcl2 motif |
deleted |
||
| LIG_HIV1-GP41 | H..NPF | 16904109 |
HIV-1 gp41 core-binding motif. |
deleted |
||
| 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 |
|
| 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 |
|
| LIG_PTB_splicing | [SG][IL]LG..P | 16936729 |
Motif essential for splicing repressor activity found in cofactors of the PTB regulatory splicing repressor (Polypyrimidine tract-binding protein). |
deleted |
||
| LIG_WW_Fe65 | PPLA | 18547980 |
Motif of GSK3beta that binds to Fe65. This interaction regulates apoptosis and phosphorylation of Tyr 216 of GSK3beta. | description updated |
deleted |
Please cite: ELM - the database of eukaryotic linear motifs (PMID:22110040)
ELM data can be downloaded and distributed for non-commercial use according to the ELM Software License Agreement