ELM candidate motifs
ELM annotation process is a tedious and time-consuming process involving critical reading of primary and secondary literature, finding motif instances,
generating multiple sequence alignments and more.
In order not to loose track of possible annotations, we keep the following list of candidate motifs.
We invite researchers to send us their feedback and expert opinion on these
classes and to contribute novel motif classes that will be added to the candidate page and ultimately be turned into full ELM classes.
Minimum requirements are at least one literature reference as well as a short description. In addition, a draft regular expression or a 3D structure showing the relevant interaction would also be helpful.
Currently 234 candidates need annotation: (Add a new candidate)
Detailed Status:| first draft: | 234 |
| Identifier | Model | References | Description | Notes | Status | |
|---|---|---|---|---|---|---|
| DEG_FEM1B_FNIP1Cys3_2 | R...C.CkYC.H | 7ROY 32941802 34562363 |
Remarkable Triple-Cys Degron binding via Zn++ coordination to E3 ligase FEM1B. Is used as part of oxidation-reduction monitoring in the cell. Binds a different surface to the FEM1B C-degrons. |
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| LIG_FERM_ERM_2 | MDW[^P][^P][^P][^P][^P][LI]F[^P][^P][LF] | 16615918;15020681 2D10;2YVC; |
The C-terminal helical motif that mediates binding to the FERM domain of Radixin, is found in NHERF-1 and NHERF-2. Binds different sites to PSGL-1, NEP, CD44 and CD43. Nice mutational analysis in the paper. Seems quite conserved in vertebrates. First two residues Met and Asp don't make direct contact. Trp is buried deep in the pocket, and Phe engaged in the second pocket with stacking interactions. Lys seems important in the +2 and +3 sites after conserved Trp and makes H-bonds with E244, additional interaction with F240 (2D10). C-terminus main chain carboxyl from Leu forms H-bond with T214 and N210 from the binding partner. | switches.elm:SWTI000333 overlaps with the motif. |
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| LIG_FERM_ERM_1 | [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. |
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| TRG_NES_CRM1rev_2 | #.#.[^P]{1,2}#[^P]{2,3}#([^P]{2,3}#) | Fung,2015 Fung,2017 35995566 5DIF 5DHA 5DHF 5DI9 |
Some CRM1-binding nuclear export motifs bind in the reverse orientation to the usual motifs. Reverse NESes include Rio4 and CPEB4 The known reverse motifs (Class 2) bind mainly as an alpha helix. There are four or five hydrophobic residues entering a hydrophobic groove of CRM1. The first two hydrophobic residues must have exact #x# spacing for reverse orientation. By contrast, for the forward orientation Class 1 motifs, the last two hydrophobic residues must have the exact #x# spacing. Class 3 forward motifs are helical and are shifted with respect to Class 1 and do not need to occupy one of the hydrophobic pockets. |
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| DEG_Kelch_KLHL20_1 | LPDLV | 31279627, 6GY5 |
BTB-Kelch E3 ligase degrading DAPK1, PML, and ULK1. Structure for DAPK1 peptide. Unusually, the bound peptide is within the DAPK1 Death Domain. |
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| LIG_HBOX_DDB1 | nx[VLtp][^P][^P][Lvfh][^P][^P][Rvahs][^P][LIVRk][^p] | 19966799 35938868 7ukn |
~13aa structural motif, that must be located inside a disordered region, and which binds to DDB1. The most important interacting residues are not fully conserved but are either hydrophobic or basic. Found in many DDB1-binding proteins such as DCAFs 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 and hCMV pUL145 which use it to hijack DDB1. Viral motifs tend to have higher affinities than cellular ones. |
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| DOC_PP2A_B55_2 | [kr]v..[vi]r | 34661528 | Docking site required for the regulatory subunit B55 of PP2A for protein dephosphorylation. |
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| DOC_PP2B_TxxP_1 | ([ST].[RK]P)|([ST][RK].P) | Li,2020, Hendus-Altenburger,2019 | Calcineurin (PP2B) preferred dephosphorylation of serine/threonine phosphorylation sites |
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| DEG_MAGE_A11_1 | [LFYW]..[^P][VIMACL][^P][^P][IV[RK][^P][LVMI][LFWY] | 33004795 6WJH |
MAGE proteins are a class of substrate adaptors for E3 ligases. MAGE-A11 recognises a helical hydrophobic degron with one key positively charged residue |
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| LIG_LxxPTP_EBH_2 | [LIVM]..PTP[ILTV] | 28552577, 29576319; 5N74 |
The LxxPTP motif is found in some +TIP proteins that bind to the EBH domain of the EB1 microtubule end-binding protein. It binds the same surface as the SxIP motif but with some EBH domain rearrangement. |
Sequence conservation is very poor and it is not clear that this motif can be annotated. |
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| TRG_ER_KDEL_2 | [KRHQSAP][DENQT][ED]L[K]{0,1}$ | 9914159 | Same as previous TRG_ER_KDEL_1 but modified to recognize the C-terminal motif in Exotoxin A in Pseudomonas as well as its closely related species. | The Lys at the C-terminal position is conserved in all Exotoxin As from P. aeruginosa as well as in Cholix toxin from V. cholerae. The position -3, counting from the C-terminal, in Exotoxin A from P. aeruginosa has a conserved Asp while all the Cholix toxins have a Glu. An exotoxin from Aeromonas hydrophila does not contain the same Lys at the last position (resembling the canonical KDEL motif) but half of the sequences (11 out of 26) have an Asp at the position -2 counting from the C-terminal. Not clear that this can be annotated as cellular KDEL motifs are not seen to tolerate c-terminal extensions. |
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| TRG_Kap121pNLS_IxK_1 | ..[IV].K.{1,2}[KRH] | 26022122, 23541588, 26173234, 15367670, 3W3X, 3W3W, 3W3Y, 4ZJ7, |
The yeast importin beta, Karyopherin 121 (Kap121p) can import proteins to the nucleus that have an NLS with a core of [IV]xK. A few ligand proteins are reliably known, including structures for the IxK motif in Nup53, Ste12, Pho4, Cdc14. | The pattern around the core needs to be defined to make a motif entry. It has a positive charge preference. |
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| LIG_CAF40_CBM_1 | LgFDPf[^P][^P][STC][^P][^P][^P]L[^P][^P]ll[^P][^P]E | 30692204 28165457 29255063 |
CBM is a long, mainly helical, linear motif in proteins which bind to the CAF40 subunit of the CCR4-NOT mRNA deadenylase complex. CBM is found in NOT4, Roquin and Bag of Marbles. |
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| MOD_CAAXbox_PGGT_1 | (([KR]{2,9})|([KR]{1,6}.[KR]{1,3})).{0,2}C.[VIL].$ | 8811180 | Specific case of prenylation by Protein Geranylgeranyl Transferase I (PGGT) |
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| LIG_SH2_IC | (Y).N | Huang,2008 | 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. |
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| MOD_P4H_1 | PPG | 10428773 12824157 19553701 27129244 14698617 26368022 |
Extracellular motif that undergoes proline hydroxylation by P4H | Particular version of XYP repeats |
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| MOD_Ime2_RPxS_1 | RP.[ST] | 17198398, 17349956, 16776651, 25310241, 24710277, 25243405, 22356909, 16954377 |
Ime2 is a yeast meiotic kinase. Although related to the CDK group, it does not recognise SPxK sites. Instead, it recognises RPxS/T sites. Substrates include CDH1. The related mammalian kinases are ICK/MRK, MAK and MOK. ICK has also been shown to preferentially phosphorylate RPxS/T sites. These three kinases are required for proper ciliary function. |
Mutations in ICK cause Endocrine-cerebro-osteodysplasia ECO). Mutations in MAK cause retinitis pigmentosa 62 (RP62). |
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| LIG_ET_KIKL_1 | [LVI][K][IFL][KR].{0,1}[LFIV] | 29567837 27291650 26858406 6BGG 2NCZ 6BGH 2ND0 2N3K |
The KIKL motif is found in proteins such as CHD4, SMCA4 and NSD3 that bind to the small three-helix ET (or NET) domain of BET proteins. This interaction creates a two-stranded sheet by beta-augmentation to a loop region. Most of the KIKL-containing proteins are themselves part of protein complexes which usually have chromatin remodelling functions. Viral proteins such as KSHV LANA and MLV-Integrase also have KIKL motifs. | ET is homologous to the AHD domain of AF9 which also binds a linear motif by beta-augmentatioN (23260655). |
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| MOD_Cx3Xbox | C....$ | 29282289 | Extension of the CAAX box. Showed to work as substrate of both FTase and GGTase-I in both yeast and mammals. | Expected instances: Sushi, nidogen and EGF-like domain-containing protein 1; Putative glycosylation-dependent cell adhesion molecule 1; Sorting nexin 4 |
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| DOC_ULK3_MIT_1 | F..L[^P][^P]L[^P][^P]RF[^P][^P]L[KR] | Caballe,2015 4WZX |
Docking motif in ESCRT-III IST1 that binds to ULK3 MIT domain enabling ULK3 to phosphorylate IST1. Part of abscission delay checkpoint for lagging chromosomes |
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| LIG_VCP_VBM_2 | [MILVAK][RK][^P][^P]R[LFWE][^P][^P][FLI][^P] | Lim,2016 18208387 5EPP |
Helical motif binding a groove in the N-terminal domain of the VCP/P97/Segregase ATPase involved in transitional ER formation and other processes including ubiquitin-proteasome targeting. The VIM motif binds the same pocket in reverse orientation. |
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| LIG_VCP_VIM_1 | R[^P](5)AA[^P](2)R[^P] | Hanzelmann,2011, 18208387, Stapf,2011, 3TIW |
Helical motif binding a groove in the N-terminal domain of the VCP/P97/Segregase ATPase involved in transitional ER formation and other processes including ubiquitin-proteasome targeting. The VBM motif binds the same pocket in reverse orientation |
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| LIG_14-3-3_5 | IRLNNAIWRAWY | Ge,2012,Sato,2016 |
A newly identified 14-3-3 binding motif identified in ChREBP protein. Unlike other 14-3-3 binding proteins, here 14-3-3 binds to a non-phosphorylated site in ChREBP with high affinity and the interaction can be activated by a free sulfate or phosphate molecules provided by the metabolites like AMP or ketone bodies.AMP binds directly to ChREBP and allosterically induces conformational changes resulting in increased affinity of ChREBP for 14-3-3and stabilization of the heterodimer in the cytoplasm of hepatocytes thus inhibiting fat synthesis during periods of ketosis. The main interaction interaction interface is between the α2 helix of the ChREBP and the positively charged patch containing a Arg-Arg-Tyr triad on the binding groove on 14-3-3. Motif is highly conserved in mammals. |
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| RTX_motif | G..G.[DN].[LVIFY]. | 19015266 27058787 17728256 8253063 |
This motif is present in several bacterial toxins, usually in 5 to 50 repeats, and are highly common in effector proteins from the type one secretion system (T1SS) (19015266). In CyaA from Bordetella pertussis, the motifs are located in a predominantly disordered region at the C-terminal of the protein. Under nanomolar concentrations of Ca2+ (as in the bacterial cytosol) the C-terminal region lacks a terciary and secondary structures. After CyaA is transported through the T1SS, the protein gets in contact with Ca2+ which is sequestered and induces the folding of CyaA into β-Rolls Ratchets (27058787). The motif has also been described in extracellular lipase from Serratia marcescens (2QUA; 2QUB), Serralysin from Pseudomonas aeruginosa, triacylglycerol lipase from P. aeruginosa (1EX9), Hemolysin from Escherichia coli, triacylglycerol lipase from Brukholderia cepacia (1OIL) and in the fungal lipase from Thermomyces lanuginosus (1EIN; 1DT3) (17728256; 8253063). |
CyaA has PDB structures: 5CVW and 5CXL |
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| LIG_Vh1_VBS_2 | DD[VMIL][MILFYPA].[TASKHCR][AVSCT]..[ILVM]...[LMTVI]..[LMV][ILVMAT]..[AIVLMT] | Park,2011 | Surface cell antigen 4 (sca4) is a protein from R. rickettsii that contains two VBSs, sca4-VBS-N and sca4-VBS-C, where the former resembles the binding of the talin or IpaA VBSs The later contains a Pro at position +14 causing a kink in the helix structure. The crystal structure of sca4-VBS-C with vinculin (3TJ6) shows that the position of the alpha-helix alpha1 in the Vh1 domain of vinculin has a dramatic movement compared to its corresponding position in other structures containing non-kinked helices (Park,2011), therefore exemplifying a new variant of a Vh1 binding-motif. |
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| LIG_IRF3_1 | [DEN]L.I(S)|[DE]{2}.[DE]L.IS | Zhao,2016 Structural and functional studies about the pLxIS motif in cellular and viral proteins. Structures of STING (5JEJ), MAVS (5JEK), TRIF (5JEK) and NSP1 (5JEO; 5JER) with IRF-3. Structure of the IRF-3 dimer (5JEM). Liu,2015 Phosphorylation of the pLxIS motif. Barro,2005 The C-terminal region of NSP1 binds IRF-3 and mediates its degradation. |
The recognition of pathogen-associated molecular patters (PAMPs) involves different pathways that can trigger convergent antimicrobial responses. Microbial double-stranded (ds)DNA in the cytosol is sensed by cGAS whcih produces the second messenger cGAMP, cGAMP binds to the adaptor protein STING which is located at the endoplasmic reticulum (ER) surface. Viral dsRNA is sensed in the cytosol by RLRs which activates the adaptor protein MAVS which is located at the mitochondria surface. Membrane anchored toll-like receptors (TLRs) 3 and 4, which recognize viral dsRNA and bacterial LPS, respectively, when activated recruit the adaptor protein TRIF. The three adaptor proteins STING, MAVS and TRIG contain a conserved motif previously refered as pLxIS that is phosphorylated by TBK1 or IKKepsilon (Liu,2015). Once phosphorylated, it binds to the transcription factor IRF-3 resulting in TBK1-dependent phosphorylation of an additional pLxIS motif in IRF-3. Phosphorylated IRF-3 forms a dimer that activates the protein (Zhao,2016). IRF-3 dimer translocates to the nucleus and positively regulates the trasncription of IFN-beta (Honda,2006). Interestingly, rotavirus is able to escape innate immune recognition by interfering with the IRF-3-dependent pathway. The rotavirus E3 ubiquitin ligase nonstructural protein 1 (NSP1) also contains the pLxIS motif which binds to the same binding region in IRF-3 in an unphosphorylated manner preventing its activation and promoting its degradation. |
In STING, the Pro at position -1 is conserved in mamals and reptiles. Leu is present in birds, opossum has a Thr at position +5. In MAVS, the motif is only conserved in mammals. Birds and fish do not have it. Tasmania devil has RLLIS. Ornithorhynchus has RLDMS and a DLNIS at 280-284. Nestor notabilis (bird) has a DLYIS at 269-273. Dipodomys (kangaroo rat) has a small duplication in the motif: EDLAISPSSSLscsEDLAISPSSSL. In TRIF, the human instance is NLEIS, which is present in 29 species in the alignment, including four legged mammals, bats and wild ducks. 12 sequences have HL.IS including primates, panda, mus musculus and fish. Other mammals had Ser, Ala, Glu, Val and Lys. Ser at position +5 was conserved in Mammals, reptiles, birds and fish. The lizard Anolis has HLEIS at 344-348. Birds have a Phe at position +2. In IRF-3, the motif is conserved in Mammals, reptiles, fish. Common marmoset (new world monkey), ginea pig, bats and european polecat have RLQIS. Tetraodon nigroviridis (fish) has SLQIS. The common marmoset, ginea pig, bat and the european polecat have DLLIS at ~227-231. Tetrodon nigrovorans has DLEIS at 209-213. In NSP1, the phosphorylation is not necessary. Substitution of Ser at position +5 did not abolish the targeting of IRF-3, however it is conserved. L486A (position +2) abolished the activity of NSP1. I488A (position +4) partially impairs the activity of NSP1. |
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| LIG_CRIB_1 | I[SG].P..{0,1}.[FA][EKRQ]H..[HT][VT][GSQ] | 7493928 First described the Cdc42/Rac interactive binding motif. 9601050 Fragments as short as 75 to 94 of PAK1 still bound to either Cdc42 or Rac. Fragments 75-105 showed binding to Q61L Rac.GTP with Kd=1.9 µM. 9660763 They calculated that the 37 aas long region of WASP (221-257) still bound to Cdc42 with a Kd of 470 nM as measured by titration. Secondary structure was only observed for the longer fragment (W13). 9774440 and 10551809 showed that the substitution of His83 (position +9) and His86 (position +12) for Leu strongly decreased binding of PAK1 with Cdc42. 9774440 PAK1 75 to 132 (which includes the CRIB motif (75-88)) did not bind Cdc42. 22653441 The binding of PAK4 and Cdc42 was demonstrated by anti-tag coimmunoprecipitation. 22362774 The beta-strand is only 5 aas long ("EIIVL"). The correct alignment starts at Ile49 in SopB (Ile12 in PAK6). The Ile in position +1 (the only one conserved) was mutated in SopB and the (22362774) and the binding to Cdc42 got disrupted. 9528787 The Ile present in all Cdc42 binders at position +1 has been mutated for Asn and the affinity decreased 3-fold. 11940652 Ser at position +2 reduces interaction with CDC42. His at position +10 reduces interaction with CDC42. 12586692 His at position +10 reduces interaction with CDC42. His at position +12 reduces interaction with CDC42. 11940652 Mutations in the CRIB motif allows Cdc42-independent kinase activity and signaling ability, indicating the CRIB motif also works in the autoinhibition of Ste20. 10802735 They obtained the NMR structure of rat Pak1 and Cdc42 with overall very low wwPDB validation scores. In general, it does not overlap with any of the other structures of Rho GTPases, for example its RMS distance to Rac3 (2QME) is 3.16. |
A linear motif of 14 to 15 residues long mediates the binding of different kinase and non-kinase proteins to the small Rho GTPases Cdc42 and Rac. The motif has been previously described as Cdc42 and Rac-interactive binding (CRIB) motif (7493928). The p21-activated kinase (PAK) proteins are serine/threonine kinases activated by Cdc42 and Rac. They play roles in cytoskeleton dynamics, cell adhesion, apoptosis and mitosis. They link integrin activation with JNK MAP kinase pathway, phosphorylate and activate MEK1. PAK orthologs have a well conserved N-terminal region. However, only the positions corresponding to the CRIB motif share conservation among paralogs. Other unrelated proteins like the actin polymerization regulator WASP and the tyrosine-protein kinase PR2 are also binders of Cdc42 and Ras (9660763; 7493928). In all these cases the presence of the CRIB motif is necessary for binding, but high affinity is only observed with additional molecular interactions that depend on an extended region C-terminal from the motif (9601050; 9660763). Several crytallographic and NMR structures have been solved of the interaction of the CRIB motif and either Cdc42 or Rac (1EES; 1E0A; 2OV2; 2ODB; 1CEE; 4MIT; 4JSO; 1NF3; 4DID; 2QME), the comprehensive analysis of these structures show that around 26 amino acids are suficient to keep a static complex structure. The CRIB motif forms a beta aumentation with the small Rho-GTPase. |
The bacterial protein SopB from Salmonella enterica binds to GDP-bound Cdc42 with a Kd=6uM +-2uM also creating a beta augmentation. However, the sequence is highly degenerated and is not covered by the current regular expression (22362774). The putative paralog of PAK in Entamoeba histolytica binds to RacC from E. histolytica. The structure (4MIT) compared to PAK6 bound to Cdc42 (2ODB) shows that the helix present at the C terminal of the crystalized region is irrelevant for the interaction with the Rho GTPase. |
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| MOD_ARK/PRK/AAK1_1 | [LI]..Q.(T)G | 12956961, Zeng,1999, Zeng,2001, Huang,2003, Ricotta,2002 |
Optimal phosphorylation site motif for mammalian AAK1 and yeast PRK/ARK kinases that are involved in the regulation of endocytosis. A more relaxed version of the motif is [L/I/V/M]xx[Q/N/T/S]xTG |
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| LIG_APP_AP2beta_1 | [FL]..G[FL].DF | Schmid,2006, 1E42 |
Motif binding to the side site of the C-terminal beta2-appendage domain of the large subunit beta2-adaptin. This interaction is part of the system for recruiting partners for assembly of clathrin-coated vesicles. |
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| LIG_MHD_FCHO_1 | DPFxxxDPFxxDPF | 27237791 25061211 |
The motif binds to mu humology domain (MHD) of FCHO with an affinity of 2μm. |
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| eIF2alpha_binding_motif | Rx[Gnl]x1-2Wxxx[Arlv]x[Dn][Rg]xRFxx[Rlvk][Ivc] | 26100893 |
The eIF2α-binding motif is characterized by the consensus sequence Rx[Gnl]x1-2Wxxx[Arlv]x[Dn][Rg]xRFxx[Rlvk][Ivc], where capital letters are preferred and x is any residue. This eIF2α-binding motif is found in the PP1 regulatory subunits GADD34, CReP, and several viral proteins including, ICP34.5, DP71L, and CNPV231. |
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| LIG_PEX19_mPTS_1 | 15133130 | PEX19 is thought to be the receptor for importing peroxisomal membrane proteins by binding to a short mostly hydrophobic peptide, the mPTS. |
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| TRG_Transportin_M9nls_1 | R..PY..P | 7730395, 15703190, 16901787, 22778397, 16179349, 4FDD, 4JLQ, 2OT8, 2Z5K, 2Z5O, 2Z5N |
Non-canonical NLS bound by transportin/karyopherin beta. Found in some RNA processing proteins, in T-box and ATF4/5 transcription factors. Always has a PY doublet, usually preceded by positively charged residues and also a weakly conserved second hydrophobic motif. Mutations in M9 class NLSes cause Di George syndrome (mutated in Tbx1) and ALS (mutated in FUS, EWS, TAF15). | Observed instances are quite variable and likely require several motif patterns to capture the range of possibilities. |
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| Lig_IntegrinA4B1_MLD | MLD | 14769041 | Extracellular alpha4beta1, alpha9beta1 and alpha7beta4 Integrin-binding motif. Motif was first identified in snake venom disintegrins. | Not sure if a native protein with MLD has been identified. |
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| LIG_RGD_High | RGDL..[LI] | Dong,2014 4UM8 4UM9 |
Integrin alphaVbeta6 binds with high affinity to a RGDLXXL/I motif within the prodomains of TGF-β1 and TGF-β3. |
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| LIG_MSL3 | AFG..[LIV]..[LIMF].{4,10}F.LPW | 21217699, 2Y0N | Long extended peptide wrapping around the MRG domain of MSL3, with one part forming a short hairpin; highly conserved hydrophobic residues (mainly Phe) insert into different hydrophobic pockets on the MSL3 surface; found in MSL1 (subunit of the male-specific lethal complex involved in gene dosage compensation); (see also literature on WDR5-binding motifs in ELM). | 21217699 discusses other proteins using similar surfaces/sequences for binding, see references therein; model presented here only describes core, should be extended at the N-terminus |
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| LIG_MOF | E.[LI].D[^P][^P][FY][^P][^P][^P]H[^P][KR] | 21217699, 2Y0M | Helical motif that binds the HAT domain of the histone acetyltransferase MOF; found in MSL1 (subunit of the male-specific lethal complex involved in gene dosage compensation) and NSL1 (subunit of the nonspecific lethal complex involved in transcription regulation and cell reprogramming) (see also literature on WDR5-binding motifs in ELM). |
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| LIG_NRBOX_AR_2 | F..LF | 15178743 | LBD-binding motif in the N-terminal region of androgen receptor that binds to coactivator-binding groove on androgen receptor (AR), competing with coactivators. This groove is deeper on AR compared to for instance estrogen receptor, which does not bind this motif. |
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| LIG_Munc18/Sec1 | D[RL].{3,4}[FL] | 23572542,20884800,21139055,11879635,12426383,1MQS | Conserved Munc18/Sec1-binding peptide present in N-terminal region of eukaryotic SNARE proteins, e.g. vertebrate syntaxin 5, yeast Sed5 and Ufe1, and arabidopsis SYP121. |
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| LIG_KC1 | F.RF | 20884800,23572542 | Motif in arabidopsis SNARE protein SYP121 required for binding to K+ channel subunit KC1; overlaps with a Sec1/Munc18-binding motif. |
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| LIG_AP_GAE_2 | W..[FW] | 14973137,17506864,2DWX | Motif in hinge region of GGA1, also in NECAP1 and amphiphysin II, that mediates interaction with the AP-1 gamma-ear domain; binds to same or overlapping site as LIG_AP_GAE_1 |
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| LIG_OST | ([FVL].C)|(C.[FVL]) | 24685145,4M91,4M92 | peptide that binds to the N33/Tusc3 (and maybe paralogous IAP/MagT1) subunit of the oligosaccharyl transferase (OST) complex to improve glycosylation efficiency; found in OST substrates; peptides can be accommodated in opposite orientations; peptide is covalently anchored to N33/Tusc3 via the cysteine residue (disulfide link); prefers Leu, Val or Phe in the -/+2 position relative to Cys; also backbone interactions |
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| LIG_CagA | 24474782, 4IRV | N-terminal domain of the Cytotoxin Associated Gene A (CagA) of Helicobacter pylori binds to a 20aa long helical motif in the Apoptosis-stimulation protein p53-2 (ASPP2). |
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| MOD_N-GLC_2 | [DE].(N)[^P][ST].. | 16619027 21209858 20523900 20847188 20581208 |
similar regular expression to MOD_N-GLC_1 but also found within bacteria and archea. | bacterial N-glycosyltransferases exhibit a more stringent specificity for the acceptor site than the eukaryotic counterpart. This restricts glycosylation to a narrow set of polypeptides |
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| CLV_MetAP1 | ^M[ACGPS][^P]... | Xiao,2010, 12665801, 18828628, 10574784, 16274222, 12475202 | Target site for cleavage of N-terminal methionine by methionine aminopeptidase MetAP1. | Overlapping substrate specificity with MetAP2 but MetAP1 cannot accommodate the larger side chains tolerated by MetAP2 (Thr and Val) in the P1' position due to its smaller active site. Disfavors acidic residues in positions P2' to P5'. His and Trp were underrepresented in P2' and P3' in the most active substrate peptides as determined by peptide library screening. Strong preference for Ala in P1'. |
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| CLV_MetAP2 | ^M[ACGPSTV][^P]... | Xiao,2010, 12665801, 18828628, 10574784, 16274222, 12475202 | Target site for cleavage of N-terminal methionine by methionine aminopeptidase MetAP2. | Overlapping substrate specificity with MetAP1 but can accommodate larger side chains of Thr and Val in the P1' position due to its larger active site. Disfavors acidic residues in positions P2' to P5'. Disfavors Trp at P2' and P3'. |
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| MOD_NatF | ^(M)[LFIWK]... | 21750686, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 | Target site for acetylation of N-terminal methionine by NatF/NAA60. See 19660095 for nomenclature. | Found only in higher eukaryotes, consequently MK termini are rarely found to be acetylated in yeast. |
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| MOD_NatE | ^(M)[KLMA]... | 3TFY, 21900231, 21383206, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 | Target site for acetylation of N-terminal methionine by NatE/NAA50. See 19660095 for nomenclature. | Specificity partially overlaps with NatB and NatC. |
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| MOD_NatD | 19332560, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 | Target site in histones H2A and H4 for N-terminal acetylation (SGRGK termini) by NatD/NAA40 after cleavage of initiator methionine. See 19660095 for nomenclature. | In vivo substrate specificity for NatD is determined by N-terminal 30-50 amino acid region in its histone substrates, instead of the first few residues (2-5) in case of the other N-acetyltransferases. |
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| MOD_NatC | ^(M)[LFIW]... | 23613772, 10545125, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 | Target site for acetylation of N-terminal methionine by NatC/NAA30. See 19660095 for nomenclature. | Might also accept a Tyr residue in the second position. Specificity partially overlaps with NatB and NatE. |
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| MOD_NatB | ^(M)[DENQ]... | 22814378, 12507466, 10545125, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 | Target site for acetylation of N-terminal methionine by NatB/NAA20. See 19660095 for nomenclature. | Specificity partially overlaps with NatC and NatE. |
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| MOD_NatA | ^([SATVCG])[^P]... | 4KVM, 19420222, 10545125, 21383206, 23912279, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 | Target site for N-terminal acetylation by NatA/NAA10 after cleavage of initiator methionine. See 19660095 for nomenclature. | There might be subtle differences in specificity between yeast and human. NatA might also target N-terminal acidic residues, likely only in higher eukaryots and when acting independently from its auxiliary protein NAA15. |
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| 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. |
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| LIG_FDF | FDF|.DW | 19285948, 2WAX, 2WAY, 23851565, 4BRU, 4BRW | Motif in regulators of mRNA decapping like Pat1 and Edc3; mediates binding to the RecA2/Helicase_C (PF00271/IPR001650) domain of yeast Dhh1 and human Ddx6 RNA helicases. Edc3 contains the FDF variant, as well as yeast Pat1, while vertebrate Pat1 has the DW variant. Interactions mediated by this motif likely regulates binding of RNA to the helicase. | In Edc3 the motif has been described as part of the FDF domain (PF09532/IPR025762), an alpha-helical domain with the conserved FDF sequence at the N-terminal. Structures show that additional binding elements determine the interactions. A helical acidic motif N-terminal to the FDF/DW motif in Pat1 binds to a second pocket on Dhh1, while a helical segment (F[DN]K) located C-terminal of the FDf motif in Edc3 binds yet another pocket on Ddx6/Dhh1. |
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| FUN_FG_nucleoporin | (FG)n | 18688269, 12065398, 12372823, 17161424, 16338415 | Motif present in nucleoporins that function as intramolecular cohesion elements imparting order to the FG domain and compacting its ensemble of structures into native premolten globular configurations. |
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| LIG_Kln1_MELT_1 | ..M[ED][LIVMF]T.. | 24066227, 24361068, 4bl0 |
Repeated semi-conserved motifs with the consensus MELT are found in Kln1/Spc105 and bind to the BUB3 beta-propeller as part of the spindle assembly checkpoint. The motifs are phosphorylated on the Thr residue by Mps1. A structure of the motif in complex with the Bub3 domain has been solved in the yeast system. | By sequence alignment, the mammalian MELT repeats might be longer than the yeast ones. The core MELT should be similar though. Backbone interactions extend beyond the core MELT motif: Pro might be excluded from some adjacent positions. |
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| Lig_CaM_1-5-10 | ...[FILVW]...[FILVW]....[FILVW] | Rhoads,1997 | Several helical motif variants can bind calmodulin, including the Ca++ independent IQ motif and the 1-8-15 and the 1-5-10 motifs. The 1-5-10 motif is defined by the hydrophobic residue spacing. Other key features are lack of proline and a preference for positive and against negative charge. | Additional info here http://calcium.uhnres.utoronto.ca/ctdb/ctdb/ http://structbio.vanderbilt.edu/cabp_database/index.html |
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| Lig_CaM_1-8-15 | [FILVW]......[FILVW].....[FILVW] | Rhoads,1997 | Several helical motif variants can bind calmodulin, including the Ca++ independent IQ motif and the 1-8-15 and the 1-5-10 motifs. The 1-8-15 motif is defined by the hydrophobic residue spacing. Other key features are lack of proline and a preference for positive and against negative charge. | Additional info here http://calcium.uhnres.utoronto.ca/ctdb/ctdb/ http://structbio.vanderbilt.edu/cabp_database/index.html |
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| LIG_SCF-TrCP1_2 | [EDST][ESTD][GAS].{1,3}[STD] | 19150432 14676825 Watanabe,2004 15845771 18354483 17387146 18378670 15917222 15767683 Zhao,2010 20858893 23948254 |
non-canonical variants of the LIG_SCF-TrCP1_1 |
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| LIG_Menin_MBM_2 | Grembecka,2010, Huang,2012 |
Bipartite interaction interface recognised by Menin. MBM1 (90nM) and MBM2 (1,400 nM) bind with different affinities but together bind with a much stronger affinity (6.8 nM). Exact residues are unknown but fall between residues 23-40. | This entry may be fused with MBM_1 in light of the crystal structures of JunD and MLL1 complexes |
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| LIG_Menin_MBM_1 | ...R{0,2)FP[GA].P | Grembecka,2010, Huang,2012, 3U85, 3U86 |
Part of Bipartite interaction interface recognised by Menin. MBM1 (90nM) and MBM2 (1,400 nM) bind with different affinities but together bind with a much stronger affinity (6.8 nM). MBM1 binds in an extended conformation. Crystal structures with MLL1 and JunD define this core part | Positive charged residues c-terminally are also critical for the motif and if possible should be added to the core motif. |
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| MOD_Citrullination | ^M{0,1}[SGAT].R. | 16567635 23818587 |
Peptidylarginine deiminase 4 (PAD4) is a Ca2+-dependent enzyme that converts arginine and methylarginine residues to citrulline. Originally identified in Histones, more recently PAD4-mediated citrullination of GSK3β has been discovered | may not be only N-terminal |
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| MOD_PKB_1 | R.R[^PRK].[ST][FY^P] | Yang,2002, 1O6L | Improved P-site motif for PKB. Position -2 cannot allow Pro due to backbone H-bond. Position -2 considered not to allow R on structural grounds: this would differentiate relative to some other basophilic kinases. Position -2 has a strong T preference too. Position +1 is probably not strong enough to demand hydrophobic residue, though clearly favouring one. GSK3beta p-site is close to optimal. |
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| Mod_PIMK_1 | R.R[RKH^PDE].[ST][G^P] | 16227208,2BZK | PIM kinases of the CAMK-related group are mediators of cytokine signaling pathways in hematopoietic cells. Their P-sites are basophilic with a preference for R at the -5 and -3 positions like some other basophilic kinases. They have a weaker preference for positive charge at -2 (and cannot tolerate P). A weak G preference is found at +1 and P is rejected. |
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| MOD_LRRK2_1 | [FY].(T).R | 21060682 | The Parkinson's kinase LRRK2 phosphosite motif derived by oriented peptide library. | Y is weaker than F at -3. K and R are generally favoured in the +1,+2,+3 positions of the motif. |
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| LIG_Neur_NXXN | N..N..L | 19580805 | N-rich motifs such as N..N..L in bearded and QN..NA in Delta reported to bind to the Neuralized E3 ligase. Motifs seem to play a role in both inhibition and activation of Notch signalling. |
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| LIG_PSI_ProlineMotif_1 | P.PPP | 15990112 | Proline-rich sequence binding to small double alpha-helical module known as PSI A,B box or PFAM DUF1897 found as two or three copies in a few RNA-binding proteins e.g. PSI, KHRP. Aromatic residues on one helical face make hydrophobic interactions with Pro residues in the peptide motif which is found in U1-70k protein of the U1 snRNP. In fly, involved in P-element transposase alternative splicing. Strong phylogenetic conservation suggests that there is a more general cellular function. | Not clear if this interaction is well enough described yet to make a motif pattern capturing the allowed Pro residue spacing and any possible additional residues. |
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| TRG_NoDS | RR[IL].{1,10}[ILVF][ILVF][ILVF] | 22284675 | Nucleolus targeting signals that results in sequestration of proteins by ncRNA |
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| 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. |
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| 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. |
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| 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. |
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| LIG_sHSP_IxI_1 | .I.[IV]. | 23188086, 23340341 |
Oligomerisation motif of alpha-crystallins and related small heat shock proteins. |
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| 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 |
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| MOD_CDK_3 | ([ST])P... | Byeon,2005 | variant motif; instance does not match current RegEx | instance in switches.elm: SWTI000284 MK67I_HUMAN (Q9BYG3) 235 241 |
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| LIG_Dynein_DLC8_2 | [KR].TMT | 17029413;16981716 | variant | instance in switches.elm: SWTI000541 MYO5A_HUMAN (Q9Y4I1) 1286 1290 |
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| CLV_CASPASE3_1 | D..D | 12637508 | relaxed Caspase3-1 cleavage site | instance in switches.elm: SWTI000550 CEAM1_MOUSE (P31809) 457 460 |
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| 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. |
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| 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. |
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| TRG_NES | Mazanka,2008 | NES |
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| LIG_BROMO_BET | (K)[GILVMF]{0,1}[^MFYLW].(K) | 2WP2 19794495 22464331 |
Diacetylation recgnition motif for bromodomain of BET family | first BRDs of the BET family |
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| LIG_BROMO | 20502673,11080160 1E6I | The Bromodomain binds acetylated lysine residues in the flexible N- and C-terminal tails of histones. |
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| TRG_NLS | Shin,2002 1594241 Duprez,1999 21092142 21182795 | non-canonical nuclear localisation signals |
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| 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 |
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| LIG_MBT | 20502673 1OYX 12842041 | Malignant brain tumor (MBT) repeats have been implicated as methyl-lysine binding modules. |
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| LIG_CHROMO | ARK[ST] | 20502673 1KNA 11859155 | Chromo domains promote binding to methylated lysines in Histone H3 tails. |
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| MOD_SUMO_PHOS | [VILMAFP](K).[ST]. | Picard,2012 | Novel Sumoylation site found in Estrogen receptor beta connected to a GSK-beta phosphorylation site |
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| 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. |
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| 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 |
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| LIG_SH2_IA | (Y)[DE][DE][AFILVWY] | Huang,2008 | 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] |
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| LIG_SH2_III | (Y)..Q | Huang,2008 | Group III comprises the STAT family of SH2 domains. |
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| LIG_SH2_IID | (Y)... | Huang,2008 | this is the generic motif for Group 2 SH2 domains. |
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| LIG_SH2_IIC | (Y)... | Huang,2008 | this is the generic motif for Group 2 SH2 domains. |
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| LIG_SH2_IIB | (Y)[ED].[AFILVWY] | Huang,2008 | 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 |
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| LIG_SH2_IIA | (Y)[AFILVWY].[AFILVWY] | Huang,2008 | 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. |
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| LIG_SH2_IE | (Y)[DEKNPR][DEKNPR][AFILVWY] | Huang,2008 | this is the generic motif for Group 1 SH2 domains. |
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| LIG_SH2_ID | (Y)[DEKNPR][DEKNPR][AFILVWY] | Huang,2008 | this is the generic motif for Group 1 SH2 domains. |
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| LIG_SH2_IB | (Y)..[AFILVWY] | Huang,2008 | 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 |
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| TRG_AP2beta_CARGO_2 | [FY]F.{6}W.[FY] | 19287005 | non-canonical AP2-beta2 binding found in isoform of PIPKIγ |
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| TRG_NES_CRM1_2 | L.{2,3}L.L | 11074002 | very general NES |
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| 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 |
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| CLV_C14_Metacaspase | 17028019, 18005666, Sundstrom,2009, 21597462 |
Metacaspases are distantly related to caspases and are found in protozoa, fungi and plants. They are involved in regulation of different cell biological processes, like programmed cell death and development. Contrary to caspases which cleave specific after aspartate, metacaspases cleave specific after arginine and lysine. Depending on their prodomain metacaspases were distinguished into type I and II. | Less is known about metacaspases' cleavage motif. Only 3 metacaspases' substrates were described. |
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| TRG_LysEnd_APsAcLL_2 | [DERQ].{2,4}L[LVI] | 18315530 Kirchhausen,1999 |
Slight variation of TRG_LysEnd_APsAcLL_1 |
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| TRG_MLS | 22178138 10837244 16616497 |
The N-terminal Mitochondrial localisation signal recognised by Tom70. | Could not define regular expression |
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| LIG_IQ_3 | [FILV]Q...[RK]G...[RK]..[FILVWYM] | Rhoads,1997 8805510 8127365 12351846 Bahler,2002 |
extended IQ motif |
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| LIG_IQ_2 | [FILV]Q...[RK] | Rhoads,1997 8805510 8127365 12351846 Bahler,2002 |
IQ-like motif. |
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| LIG_BIR_internal | A.[AP]. | 14523016 | Internal BIR-binding site. In this case, precursor mitochondrial localisation signal is removed exposing BIR site |
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| LIG_PI(4,5)P2 | [KR].{3,4}K.[KR][KR] | 9891784,Kojima,2004 | lipid binding motif for PI(4,5)P2 |
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| LIG_Filamin_2 | Y..A[VIL]...[VIL] | 16455489 2BRQ |
Based on integrin binding to filamin |
No mention of importance of threonines defined in LIG_Filamin |
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| LIG_TPR_4 | [ST].[ST] | 21454478 3Q4A |
phosphorylated version of LIG_TPR found in Smad 1/5 |
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| LIG_TPR_3 | K[IL].{0,2}Q | 18759457 17942943 |
internal TPR binding motif with similatities found in androgen receptor and vpu | unsure of veracity |
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| 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 |
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| LIG_MIU | [DE][LIVY].[LIV]A..[LIVY]..[DE]{DE] | 16499958 2C7N 2C7M 19217402 |
MIU (motif interacting with ubiquitin; also known as IUIM or inverted UIM) |
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| 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. |
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| LIG_DUIM | [DE].[LIVY]..A[LIVYM]A.S.[SA][DE] | 16462748 2D3G | double sided ubiquitin interacting motif |
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| LIG_UIM | [DE][DE]..[ILVY]..A[ILVY].S.. | 16462748 12970172 1Q0V 2D3G 12750381 1O06 | Ubiquitin interacting motif |
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| MOD_N-GLC_3 | NG. | 20510933 21978957 | Non-canonical N-glycosylations sites found in the mouse glycoproteome |
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| MOD_N-GLC_4 | N.V | 20510933 21978957 | Non-canonical N-glycosylations sites found in the mouse glycoproteome |
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| LIG_PCNA_PIP_2 | ...[LIM][DE].[FHY][FHY]. | Hishiki,2009, 2ZVM,Kim,2010,Shibutani,2008 | Non-canonical PIP box, missing the p1 glutamine. Mediates binding to PCNA. Found in Polη, Polκ. | The PIP boxes of Xic1 in X. laevis and E2F in D. melanogaster overlap the PIP degron LIG_CRL4_Cdt2_1 and LIG_CRL4_Cdt2_2, respectively. |
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| 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 |
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| LIG_WW_Nedd4L | .(S)P.L(S)PN | Aragon,2011, 2LAJ | Motif in Smad3 that binds to the third WW domain of Nedd4L. Phosphorylation of Smad3 by CDK8/9 and GSK3 recruits ubiquitin ligase Nedd4-like via its third WW domain; second WW domain displaces Pin1 at WW motif upstream; leads to Smad3 destruction. |
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| MOD_Geranyl_CAAXbox_1 | (C).[LIVM][ILMV]$ | 12702202 | Motif modified by Geranylgeranyltransferase I (GGT1). | Should replace current MOD_CAAXbox to define specificity. |
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| MOD_Farnesyl_CAAXbox_1 | (C).[LIVM].$ | 12702202 | Motif modified by Farnesyltransferase. | Should replace current MOD_CAAXbox to define specificity. |
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| LIG_DCUN1_1 | (M)[IL].L | Scott,2011 3TDZ | Acetylated N-terminal methionine motif that mediates binding to the DCUN domain of E3 ligase DCN1 found in E2 ligase Ubc12. |
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| 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. |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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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. |
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| 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. |
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| 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. |
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| LIG_Glycolytic_Aldolase | W[DE]{2,3}W | 3LGE 20129922 | Motif that mediates binding to Aldolase A |
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| LIG_SH3_9 | SAMP | 18786926 20509626 2RQU | a non-canonical SH3 binding motif associated binding to ASAP1 and colocalized at microtubule ends. |
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| LIG_Alpha-synuclein | .DVF. | 19762560 | interaction with coiled coils of Synphilin-1 |
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| LIG_Actin_DMD | LK..E[ST] | 9883911 | actin binding motif found in the Dp71 dystrophin isoform |
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| 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. |
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| LIG_BTB_SMRT | [GL][IV][AT]T[IV]KE[AM]GRSIHEIPR | 14690607, 1R2B | Motif mediating binding of BCL6 BTB domain to SMRT |
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| LIG_EAR | 20935498 11487705 | EAR motif mediates transcriptional repression of plant genes via recruitment of a histone deacetylase complex, which leads to chromatin modification. |
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| TRG_Golgi | 21283809 | potential Golgi-retention motif and a number of conserved motifs with unknown function |
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| 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 |
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| 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 |
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| MOD_acetyl_E2ligase_1 | [KR]R[IL].KE | 21791702 | Motif found associated with the acetylation of ubiquitin E2 ligases |
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| 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 |
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| 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 |
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| LIG_Filamin | ..(T)TT.. | 20332112,Takala,2008, 2V7D | Motif recognized by Filamin. First threonine must not be phosphorylated. | Molecular switch. See LIG_Talin and LIG_14-3-3-3 (latter might need updating of regex as does not cover binding motif in integrins mentioned in 18550856) |
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| 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) |
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| 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 |
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| 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. |
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| LIG_FERM_2 | L...M..L..LM..L..IT | Hirano,2011,Wei,2011, 3PZD | Large cargo recognition helix in DCC, Ngn and Fz1A that binds to the FERM domain of Myosin-X. |
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| 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. |
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| LIG_CORNRBOX_2 | [IL]..[ILV][IL]..[ILVYF] | Phelan,2010,3N00 | An improved definition of the CoRNbox motif based on structural studies from SMRT and N-Cor. Should update current entry rather than make new entry as they are overlapping. |
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| 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). |
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| 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. |
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| MOD_phos_AURORA | R.([ST]) | 21712546,Alexander,2011 | Canonical motif phosphorylated by Aurora kinase A/B |
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| 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) |
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| 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) |
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| MOD_HEME | CP[ILMVFY] | 7835342 | Short sequence that has been shown to bind heme and is repeated up to 6 times. |
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| 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. |
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| 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 |
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| 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. |
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| 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 |
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| LIG_Cdc20_Spo13 | L.E...N | 17493939 | Degron in the yeast meiosis-specific protein SPO13 recognised by the cdc20 subunit of the APC. |
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| MOD_SMAD | (S)[IVLM](S)$ | 9346908,18387785 | C-terminal phosphorylation motif found in receptor-activated Smads. Phosphorylated by TGF-beta1 kinase after its activation |
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| 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). |
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| LIG_N_degron_Doa10_Ac | ^([MAVSTC]) | 20110468 | Acetylated N-terminal degron signal recognized by ubiquitin ligase Doa10. Promotes proteosomal degradation. |
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| 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. |
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| 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. |
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| MOD_LammerK | (RS)n | 11827553,1577277,8772383 | Many Lammer kinases (clk1-4, Doa, PK12) phosphorylate (RS)n motifs, regulating splicing. |
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| 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. |
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| TRG_TGN | YW | 16978406 | Retrograde endosome to trans-Golgi network motif. |
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| TRG_Parasite_HT | R.L.[EDQ] | Dou,2008,19170882 | Core motif for N terminal host-targeting (HT) motif composed of 11 amino acids that is found in Plasmodium and other parasites. |
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| 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. |
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| TRG_nucleolus | 10469277,10050887,9731210 | Nucleolar targeting signals. |
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| TRG_Mit | 11381593 | Mitochondrial targetting peptides. |
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| TRG_ERM-PM | RGGKYSV | 17995939 | Motif responsible for the recruitment of ERM proteins to the plasma membrane in neurogenesis. |
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| TRG_Dendritic | LLY..[FYW] | 16988049 | Dendritic targeting motif. |
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| TRG_TAT | [ST]RR.FLK | 16987314 | Tat export consensus motif. |
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| TRG_chloroplast | 10998602 | Chloroplast transit peptides. |
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| MOD_Prk1p_1 | [LVIM]....(T)G | Huang,2003,11694597,19220811 | Motif modified by Prk1p, a yeast kinase localised at cortical actin patches and regulating endocytosis. Substrates include epsins and the Bni1p formin. |
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| MOD_methylation | 8366133 | Modification sites in histone tails and nucleolin. |
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| MOD_MegPhos | PPPSP | 17555532 | Necessary for phosphorylation of Megalin, possibly by GSK3. |
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| TRG_PEXEL_VTS | 16046186 | Export motif for RBC stage of the malaria parasite. Similar motif in potato blight. |
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| MOD_acetylation | 10656693,10607594,9744860,9774110,9809067 | Acetylation targets in the nucleus beyond histone tails: p53, HMG I/Y, TCF, etc. |
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| LIG_TRADD | YYD$ | 9356494 | Tumor necrosis factor receptor-associated death domain protein (TRADD) binding motif in LMP1 |
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| LIG_Sap1_Bbox | F.L..L | 11406578 | SRF binding motif with beta-augmentation core. |
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| LIG_R3IM | [DE][DE][DE]EFE[DE] | 18775730 | Motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. |
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| 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. |
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| 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. |
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| LIG_Notch | DSL | 17006545 | Conserved N-terminal motif in Notch ligands. |
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| LIG_MYPT1 | Y.Y | Terrak,2004 | Motif on PP1delta reciprocating the RV.F motif on the targeting subunit of MYPT1. MYPT1 also has an N-terminal helical motif interacting with PP1delta. |
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| LIG_MIT_MIM2 | [ILMV]P[DE]VP[ST]..LP | Kieffer,2008, 2K3W | VPS4 MIT domain binding "MIM2? motif found in a subset of ESCRT-III subunits |
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| 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. |
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| 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 |
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| TRG_Paranodin | PGY | 17093057 | Paranodin trafficking repeat motif. |
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| LIG_PKC | [YF][SA][VI](Y)[QR].[YF]. | 15851033 | Phosphotyrosine motif in CDCP1 binding to the PKCd C2 domain. |
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| LIG_PHDfingers_H3 | ^...K | 16728977 | NURF and ING types of PHD finger bind histone H3 trimethylated lysine. |
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| TRG_VTS | R.L.[EQ] | Hiller,2004,Marti,2004 | Vacuolar protein export signal. |
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| LIG_CKB_1 | M.E.L.LC(ST)G.F | 15707391,12545175 | Triple phosphorylated docking motif in Claspin that binds checkpoint kinase CHK1 |
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| LIG_FF | 12381297,16253993 | Phosphorylated and possibly other motifs bind FF domains. Notably the RNA polII CTD. |
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| LIG_AnkyrinG | [VA]P[IL]A..E[SD]D | 12716895,12829783 | A conserved 9-amino acid motif required for ankyrinG binding. |
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| LIG_AP2alpha_3 | W..[FW] | 14565955 | An AP-2 adaptor interaction motif initially identified in the long-splice isoform of Synaptojanin1. |
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| LIG_IntA3B1 | NVR | 17034138 | Integrin a3b1 binding motif in thrombospondin. |
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| 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 |
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| 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. |
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| 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). |
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| LIG_FERM | RSLE | 17045809 | A FERM domain binding motif in neurofascin. |
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| 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. |
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| LIG_chromoshadow_EMSY | [VILMF].[VILMF].[VILMF]..[VILMF] | 16615912 | Motif that binds to HP1 chromoshadow domains from EMSY. |
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| 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. |
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| 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. |
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| 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. |
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| LIG_Abox | Littlepage,2002 | Another destruction box proposed in Aurora A kinases. |
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| LIG_COPII | YNNSNPF, L..LE, D.E | 12941276,15093828 | Motifs involved in vesicle budding interactions of SNARES with COPII (subunits sec23/24). |
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| LIG_integrin_TGFbeta | DL..L | 14572313 | Integrin binding motif in TGFbeta. |
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| 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. |
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| FUN_UBX | QA | 16267091 | Motif is present in Drosophila Ubx family of HOX genes and with pleiotropic functions in development. |
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| LIG_clathr_ClatBox_Cter | L[IVLMF].[IVLMF]$ | 10449404 | Variant clathrin box in yeast found at carboxy termini of e.g. some epsins. |
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| FUN_Synaptotagmin | KK...K | 16987956 | Motif required for efficient synaptic transmission. |
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| FUN_Pin1_Isomerisation | P[ST]P | 12571275 | Pin1 isomerization motif. |
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| LIG_ERCC1 | D[ST]G[AG]GF | 17948053 | Used by XPA to recruits ERCC1-XPF to nucleotide excision repair complexes |
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| LG_CyclophinA | FGP.LP | 15845542 | Motif proposed to bind Cyclophin A. |
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| FUN_GPIanchor | 11814051,11677780,7482705 | Glycosylphosphatidylinositol extracellular plasma membrane anchor. |
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| FAM_apoptotic | XX...DD....D | Motif found in apoptosis induction proteins: GPP synthases, Nox-a, Bad, Bid, Bik, yt-ppy-a, s81f. |
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| 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. |
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| CLV_GxGD | G.GD | 20021564 | Motif that could be evolutionary conserved to allow cleavage of all possible gamma-secretase substrates. |
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| LIG_CtBP_2 | RRT..PPAL | Nardini,2003 | Another motif that binds to CtBP. |
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| 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. |
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| FUN_Aurora | 14752279 | Double motif in TPX2 regulating Aurora kinase activity |
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| 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. |
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| 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. |
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| LIG_integrin_extracell | LDV | Belkina,2009 | Another extracellular integrin binding motif. |
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| LIG_alphaActin | FGPVVA | 1142354 | Actin binding motif in plaque protein zyxin. Said to require alpha-actinin dimerisation. |
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| 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. |
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Please cite:
The Eukaryotic Linear Motif resource: 2022 release.
(PMID:34718738)
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement