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Caspace 11 Cleavage Site

Species:
Human
E:{ILVP}EHD
L:{ILVP}EHD
80S:{ILMVP}[EDQ][HY][DNE]
80W:{ILMVP}[EDQK][HYNQ][DNE]
35S:{ILVMFP}[EDQ]H[DE]
35W:{ILVMFTP}[EDQK][HMN][DNE]
Kang et al (May 2000) J Cell Biol. 149(3): 613-622
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Cleavage site for Caspase 11 determined through scanning combinatorial library method. This paper also suggest Caspace 8 & 9 also cleave this motif.
Caspase 7 Cleavage site

Species:
Human
E:GELE
L:GEX[DE]
80S:G[EDQ][LIM][EDQ]
80W:G[EDQK][LIMV][EDQK]
35S:G[EDQ][LIMFV][EDQ]
35W:[GNS][EDQK][LIMFV][EDQK]
Ethell et al Biochimica et Biophysica Acta (BBA) Volume 1541, Issue 3, 19 December 2001, Pages 231-238
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Consensus sequence for Caspase 7 Cleavage site. Considered non-consensus as most have EXD motifs.
GYF Ligand (a)

Species:
Human
E:PPPPGHR
L:[RKG]XXPPGX[RK]
80S:PPPPG[HY][RK]
80W:PPPPG[HYNQ][RKQ]
35S:PPPPGH[RKQ]
35W:PPPP[GNS][HMN][RQK]
Freund C., Et. al., (2002) Dynamic Interaction of CD2 with the GYF and the SH3 Domain of Compartmentalized Effector Molecules, The EMBO Journal (2002) November 15; 21(22): 5985-5995
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The PPPPGHR motif facilitates the binding of the GYF domain of CD2BP2 with the motif found on CD2. It is also shown that the SH3 domain of FYN interacts with this motif.
MAPK Docking Ligand

Species:
Human
E:[R,K]X(1-5)[R,K]X(1-9)LXLX(1-9)[AVFGPMIL][AVFGPMIL][AVFGPMIL]
L:[R,K]X(1-5)[R,K]X(1-9)LXLX(1-9)[AVFGPMIL][AVFGPMIL][AVFGPMIL]
80S:{RKQ}X{0,5}{RKQ}X{1,9}[LIM]X[LIM]X{1,9}{AVIFYPML}{AVIFYPML}{AVIFYPML}
80W:{RKQE}X{0,5}{RKQE}X{1,9}[LIMV]X[LIMV]X{1,9}{ASVILMFYP}{ASVILMFYP}{ASVILMFYP}
35S:{RKQ}X{0,5}{RKQ}X{1,9}[LIMFV]X[LIMFV]X{1,9}{AVILFYPM}{AVILFYPM}{AVILFYPM}
35W:{RQKE}X{0,5}{RQKE}X{1,9}[LIMFV]X[LIMFV]X{1,9}{ASVILMFTYWPH}{ASVILMFTYWPH}{ASVILMFTYWPH}
Sharrocks A. et al. (2000) Docking Domains and Substrate Specificity Determination for MAP Kinases, Trends Biochem. Sci. 25, 448-453
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Common Docking (CD) domains of MAP kinases interact with docking domains signified by a basic region followed by LXL followed by three consecutive hydrophobics. Example proteins include ELK-1 and c-Jun transcription factors.
PDZ Class I Ligand

Species:
Human
E:{ST}X{VL}-COOH
L:{ST}X{VL}-COOH
80S:{SAT}X{VILM}-COOH
80W:{SATN}X{VILM}-COOH
35S:{ST}X{VILMF}-COOH
35W:{STAGV}X{VILMFT}-COOH
Harris BZ, Lim WA (2001) Mechanism and Role of PDZ Domains in Signaling Complex Assembly
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PDZ Class I Ligand Domains usually interact with the PDZ "Carboxylate-binding loop" motif {RK}XXXGLGF. Two known members of this motif include: Syntrophin and PSD-95#1,2
PTB Ligand Motif

Species:
Human
E:NPXY
L:NPXY
80S:[NDE]PXY
80W:[NDES]PXY
35S:NPXY
35W:[NDQGH]PXY
Farooq A. et al. (1999) Phosphotyrosine Binding Domains of Shc and Insulin Receptor Substrate 1 Recognize the NPXpY Motif in a Thermodynamically Distinct Manner. JMBC 274 10 pp 6114-6121, March 1999
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The Phosphotyrosine binding domains (PTB) recognize an NPX-Phospho-Y motif. Additional N-terminal residues guide specificity. For Example IRS binding is enhanced by hydrophobic residues 6 to 8 residues n-terminal to the phospho-Y.
SH2 - Nck1/Nck2 Ligand

Species:
Human
E:YDE[PDV]
L:YDE[PDV]
80S:Y{EDQN}{EDQN}{PVI}
80W:Y{EDQKN}{EDQKN}{PVILM}
35S:Y{EDQ}{EDQ}{PVIL}
35W:Y{EDQKN}{EDQKN}{PVILMFT}
Frese S, et. al. (2005) The Phosphotryosine Peptide Binding Specificity of Nck1 and Nck2 Src Homology 2 Domains.
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Requires a Phospho-Tyrosine for binding. The Nck1 and Nck2 SH2 Domains are shown to bind to the motif Phospho-Y - D-E-[PDV]
SH2 Group I Ligand

Species:
Human
E:Y[RNDQEHKST][RNDQEHKST][AVFPMIL]
L:Y[RNDQEHKST][RNDQEHKST][AVFPMIL]
80S:Y{RKNDEQHYSAT}{RKNDEQHYSAT}{AVIFYPML}
80W:Y{RKQNDESHYAT}{RKQNDESHYAT}{ASVILMFYP}
35S:Y{RKQNDEHST}{RKQNDEHST}{AVILFYPM}
35W:Y{RQKNDGHEMSTAV}{RQKNDGHEMSTAV}{ASVILMFTYWPH}
SongYang Z, Cantley L, et. al. (1994) Specific Motifs Recognized by the SH2 Domains of CSK, 3BP2, fps/fes, GRB-2, HCP, SHC, Syk, and Vav, Molecular and Cellular Biology, Apr 1994, p2777-2785
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Requires a Phospho-Tyrosine in the first position. Type I SH2 proteins include GRB2, Csk, fps/fes, Syk and 3BP2 and bind the motif Phospho-Y, Hydrophilic, Hydrophilic, Hydrophobic.
SH2 Group II Ligand

Species:
Human
E:YMEP
L:YMEP
80S:Y[MIL][EDQ]P
80W:Y[MILV][EDQK]P
35S:Y[ML][EDQ]P
35W:Y[MLHIWV][EDQK]P
SongYang Z, Cantley L, et. al. (1994) Specific Motifs Recognized by the SH2 Domains of CSK, 3BP2, fps/fes, GRB-2, HCP, SHC, Syk, and Vav, Molecular and Cellular Biology, Apr 1994, p2777-2785
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Requires a Phospho-Tyrosine in the first position. The Group II ligand has only been found to interact with the Vav protein's SH2 domain.
SH2 Group III Ligand

Species:
Human
E:Y[AVFPMIL]X[AVFPMIL]
L:Y[AVFPMIL]X[AVFPMIL]
80S:Y{AVIFYPML}X{AVIFYPML}
80W:Y{ASVILMFYP}X{ASVILMFYP}
35S:Y{AVILFYPM}X{AVILFYPM}
35W:Y{ASVILMFTYWPH}X{ASVILMFTYWPH}
SongYang Z, Cantley L, et. al. (1994) Specific Motifs Recognized by the SH2 Domains of CSK, 3BP2, fps/fes, GRB-2, HCP, SHC, Syk, and Vav, Molecular and Cellular Biology, Apr 1994, p2777-2785
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Requires a Phospho-Tyrosine in the first position. Type III SH2 proteins include HCP and SHC and bind the motif Phospho-Y, Hydrophobic, any, Hydrophobic.
SH3 Class I

Species:
Human
E:[RK]XXPXXP
L:[RK]XXPXXP
80S:[RK]XXPXXP
80W:[RKQ]XXPXXP
35S:[RKQ]XXPXXP
35W:[RQK]XXPXXP
Shawn S. C. Li, (2005) Specificity and Versatility of SH3 and Other Proline-Recognition Domains: Structural Basis and Implications for Cellular Signal Transduction, Biochem, J. 390, 641-653
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Class I SH3 Ligands typically bind the R/KXXPXXP motif. Class I SH3 containing proteins include SRC, YES, AB1 and Grb2 among others.
SH3 Class II

Species:
Human
E:PXXPXR
L:PXXPX{RK}
80S:PXXPX[RK]
80W:PXXPX[RKQ]
35S:PXXPX[RKQ]
35W:PXXPX[RQK]
Shawn S. C. Li, (2005) Specificity and Versatility of SH3 and Other Proline-Recognition Domains: Structural Basis and Implications for Cellular Signal Transduction, Biochem, J. 390, 641-653
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Class II SH3 Ligands typically bind the PXXPXR/K motif. Class II SH3 containing proteins include PLC-Gamma, P53bp2, Cortactin and Crk-N, among others.
SH3 Ligand Motif (a)

Species:
Human
E:RKXXYXXY
L:RKXXYXXY
80S:[RK][KRQ]XX[YHF]XX[YHF]
80W:[RKQ][KRQE]XX[YHF]XX[YHF]
35S:[RKQ][KR]XX[YFW]XX[YFW]
35W:[RQK][KRE]XX[YFW]XX[YFW]
Shawn S. C. Li, (2005) Specificity and Versatility of SH3 and Other Proline-Recognition Domains: Structural Basis and Implications for Cellular Signal Transduction, Biochem, J. 390, 641-653
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The SH3 Ligand motif RKXXYXXY was shown in the interaction between SKAP55 and the SH3 domains of Fyn and Fyb.
SH3 Ligand Motif (b)

Species:
Human
E:PXXDY
L:PXXDY
80S:PXX[DNE][YHF]
80W:PXX[DNE][YHF]
35S:PXX[DE][YFW]
35W:PXX[DNE][YFW]
Shawn S. C. Li, (2005) Specificity and Versatility of SH3 and Other Proline-Recognition Domains: Structural Basis and Implications for Cellular Signal Transduction, Biochem, J. 390, 641-653
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The SH3 Ligand motif PXXDY was shown in the interaction involving motif bearing Eps8 and its binding partner.
Sumoylation Site

Species:
Human
E:[VFMIL]KXE
L:[AVFPMIL]KX[ED]
80S:{VIFYML}KX[EDQ]
80W:{VILMFY}KX[EDQK]
35S:{VILFYM}KX[EDQ]
35W:{VILMFTYWH}KX[EDQK]
Rodriquez, M, et al (2001) SUMO-1 Conjugation in Vivo Requires Both a Consensus Modification Motif and Nuclear Targeting, J. Biol. Chem. 276, 12654-12659
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Sumoylation requires both the motif - Hydrophobic-K-X-E and for the protein to be localized in the nucleus.
Sumoylation-Phos-S site

Species:
Human
E:[VFMIL]KXEXXSP
L:[AVFPMIL]KX[ED]XXSP
80S:{VIFYML}KX[EDQ]XXSP
80W:{VILMFY}KX[EDQK]XXSP
35S:{VILFYM}KX[EDQ]XXSP
35W:{VILMFTYWH}KX[EDQK]XXSP
Hietakangas, V., et al, (2006) PDSM, a motif for Phosphorylation-dependent SUMO modification, Proc. Nat. Academy of Sciences, V. 103, 45-50, Jan. 3 2006
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Sumoylation on a SUMO-Phos-S site requires Phosphorylation of the Serine in the motif - Hydrophobic-K-X-E-X-X-S-P
WW L-Group Ligands

Species:
Human
E:PPLPP
L:PPLPX
80S:PP[LIM]PX
80W:PP[LIMV]PX
35S:PP[LIMFV]PX
35W:PP[LIMFV]PX
Otte L, et al, (2002) WW Domain Sequence Activity Relationships Identified Using Ligand Recognition Propensities of 42 WW Domains.
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Members of L Group WW domains include hGAS7 and PRP40-2
WW P-Group Ligands

Species:
Human
E:[PGAVLI]PPPPP
L:[PGAVLI]PPPPP
80S:[PGAVILM]PPPPP
80W:[PGASVILM]PPPPP
35S:[PGAVILMF]PPPPP
35W:[PGNSAVILMFT]PPPPP
Otte L, et al, (2002) WW Domain Sequence Activity Relationships Identified Using Ligand Recognition Propensities of 42 WW Domains.
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Members of P Group WW domains include hPIN1 and yESS1.
WW Ra-Group Ligands

Species:
Human
E:[PAVFMIL]P[PG]PPR
L:PXPPR
80S:{PAVIFYML}P{PG}PP[RK]
80W:{PASVILMFY}P{PG}PP[RKQ]
35S:{PAVILFYM}P{PG}PP[RKQ]
35W:{PASVILMFTYWH}P{PGNS}PP[RQK]
Otte L, et al, (2002) WW Domain Sequence Activity Relationships Identified Using Ligand Recognition Propensities of 42 WW Domains.
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Members of R-alpha Group WW domains include hHYP109, hPQBP1, and hFE65 among others.
WW Rb-Group Ligands

Species:
Human
E:[PAVFMIL]PPRGXP
L:[PAVFMIL]PPRGXP
80S:{PAVIFYML}PP[RK]GXP
80W:{PASVILMFY}PP[RKQ]GXP
35S:{PAVILFYM}PP[RKQ]GXP
35W:{PASVILMFTYWH}PP[RQK][GNS]XP
Otte L, et al, (2002) WW Domain Sequence Activity Relationships Identified Using Ligand Recognition Propensities of 42 WW Domains.
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Members of R-beta Group WW domains include FBP21-1 and FBP21-2. Stronger binding can occur in a PPPRGPPP motif.
WW S/T-Group Ligands

Species:
Human
E:[AVFPMIL][AVFPMIL][ST]PP
L:XX[ST]PX
80S:{AVIFYPML}{AVIFYPML}{ST}PP
80W:{ASVILMFYP}{ASVILMFYP}{ST}PP
35S:{AVILFYPM}{AVILFYPM}{ST}PP
35W:{ASVILMFTYWPH}{ASVILMFTYWPH}{ST}PP
Otte L, et al, (2002) WW Domain Sequence Activity Relationships Identified Using Ligand Recognition Propensities of 42 WW Domains.
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Members of pS/pT Group WW domains require at a minimum a Phospho-Serine or Phospho-Threonine followed by a proline. Members of this group include hSmurf1, yTIN1, hHYP109 and others.
WW Y-Group Ligands

Species:
Human
E:PPXY
L:PPXY
80S:PPXY
80W:PPXY
35S:PPXY
35W:PPXY
Otte L, et al, (2002) WW Domain Sequence Activity Relationships Identified Using Ligand Recognition Propensities of 42 WW Domains.
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Y Group WW domains typically bind Tyrosine or Phospho-tyrosine PPXY motifs. Members of this group include YAP65, WWOX1, SMURF1, RSP5 and others.