The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Phosphotyrosine ligands bound by SH2 domains
Functional site description:
Src Homology 2 (SH2) domains are small modular domains found within a great number of proteins involved in different signalling pathways. They are able to bind specific motifs containing a phosphorylated tyrosine residue, propagating the signal downstream by promoting protein-protein interactions and/or modifying enzymatic activities. Different families of SH2 domains may have different binding specificity, which is usually determined by a few residues C-terminal with respect to the pY (positions +1 to +4). Non-phosphorylated peptides do not bind to the SH2 domains. Several different binding motifs are known, for example: pYEEI (Src-family SH2 domains), pY [IV].[VILP] (SH-PTP2, phospholipase C-gamma), pY.[N] (GRB2). The interaction between SH2 domains and their substrates is however dependent also on cooperative contacts of other surface regions.
ELMs with same func. site: LIG_SH2_CRK  LIG_SH2_GRB2like  LIG_SH2_NCK_1  LIG_SH2_PTP2  LIG_SH2_SFK_2  LIG_SH2_SFK_CTail_3  LIG_SH2_STAP1  LIG_SH2_STAT3  LIG_SH2_STAT5  LIG_SH2_STAT6 
ELM Description:
SRC-family kinases (SFKs) play key roles in metazoan cell signalling by relaying growth and cell adhesion signals from cell surface receptors at the plasma membrane (Shah,2018). SFKs contain a Src homology 2 (SH2) domain that mediates binding to phosphotyrosine-containing motifs (LIG_SH2_SFK_2) present in SFK substrates and regulators. These interactions regulate SFK activation, promote substrate phosphorylation and localise SFKs to membrane domains. A related C-tail motif (LIG_SH2_SFK_Ctail_3) mediates autoinhibitory interactions that inhibit kinase activity (Lipsick,2019).

The SH2 domain is made up of 4 antiparallel β sheets flanked by two α helices. SH2 motifs bind in an extended conformation perpendicular to the central β sheets. The SFK SH2 domain specificity is dictated by the YβD5 residue, and the motif pattern is derived from crystal structures and sequence preferences known from SPOT arrays, mutagenesis and motif instances. The two-pronged interaction involves conserved interactions of pTyr with the pTyr binding pocket and insertion of the pY+3 residue into the hydrophobic pY+3 pocket (Gilmer,1994). The pY+1 and pY+2 residues are oriented in opposite directions and place the peptide in an extended conformation with the pY+1 backbone hydrogen bonded to the SH2 domain. In the high affinity pYEEI motif, E at pY+1 forms favourable electrostatic interactions with LysβD3 and its aliphatic side chain packs against TyrβD5 (Gilmer,1994). The pY+1 position also accepts hydrophobic and polar amino acids. The pY+2 position tolerates substitutions, with negative residues or pTyr (as seen in the double pY PDGFR 579pYIpYV582 motif) making favourable interactions with ArgβD’1 (Lubman,2003). The pY+3 pocket binds hydrophobic residues with ILV making optimal interactions (Gilmer,1994; Bradshaw,1998). A strong residue must be found at either pY+1 or pY+3. Negative charge is preferred flanking the core motif (Alonso,1995) and positive residues are excluded at the N-terminus.
Pattern: [^KR][^KR](Y)([DEVYI][^KRH][ILVF]|[DEVYI][^KRH][AQPMCW]|[NQSTAFL][^KRH][ILVF])((.{0,3}[DE])|.|$)
Pattern Probability: 0.0008808
Present in taxons: Bacteria Bos taurus Cavia porcellus Gallus gallus Homo sapiens Mesocricetus auratus Metazoa Mus musculus Sus scrofa Viruses
Interaction Domains:
  • SH2 (PF00017) SH2 domain (Stochiometry: 1 : 1)
  • SH2 domain (IPR000980) The Src homology 2 (SH2) domain is a protein domain of about 100 amino-acid residues first identified as a conserved sequence region between the oncoproteins Src and Fps (Stochiometry: 1 : 1)
o See 20 Instances for LIG_SH2_SFK_2
o Abstract
The Src Homology 2 (SH2) domain is a major protein interaction module that is central to tyrosine kinase signaling. Over 120 SH2 domains are predicted in the human genome (Liu,2011). Among SH2 domain-containing proteins are kinases, phosphatases adaptors, ubiquitin ligases, transcription factors, guanine nucleotide exchange factors. The many processes involving SH2 domains range from mitogenic signaling to T cell activation. Mutations identified in many SH2 domain-containing proteins as well as the SH2 domain itself are associated with human diseases ranging from cancers, diabetes, to immunodeficiencies.
SH2 domains are phosphotyrosine recognition domains, often mediating transient interactions with target proteins. The binding affinity of an SH2 domain to a pTyr containing ligand is moderate, with the typical affinity range between 0.1 µМ to 10 µМ for equilibrium dissociation constant values (Kd) (Kaneko,2012).
The structure of the SH2 domain consists of a central antiparallel β-sheet formed by three or four β strands flanked by two α helices. In the canonical mode of SH2 binding, regions on either side of the central β sheet are involved in ligand binding. The N-terminal region is most conserved and contains the pTyr binding pocket. The C-terminal half of the SH2 domain exhibits greater structural variability and provides a platform for accommodating different kinds of SH2-binding motifs. Three loops surround the peptide binding pocket and are important for specificity: Because these loops can be flexible, considerable variation in peptide binding can apply for any given SH2 domain. For the majority of experimentally solved SH2:peptide ligand complex structures, the bound pTyr peptide forms an extended conformation and binds perpendicularly to the central β strands of the SH2 domain. However motifs that form alternative conformations are also identified as in the case of the GRB2 SH2 domain binding motif (Nioche,2002) where the motif forms a β-turn upon binding. Grb2 is a good example of a bifunctional adaptor protein that brings proteins into close proximity, allowing signal transduction through proteins that can span different compartments.
SPOT arrays provide an overview of different SH2 specificities (Huang,2008) although it is clear that they do not fully capture all the possible motifs for any given SH2. SH2s fall into groups with related specificities such as the GRB2-like set with a preference for YxN, the Src-like family with a preference for Y--# or the unique Stat3 YxxQ preference. SPOT arrays indicate that some SH2s might have quite poor specificity, for example PLCγ1_C and GRB7: These may be quite promiscuous. A large set of SH2 motif patterns has been made available, based on the SPOT arrays and other available data [Samano-Sanchez,2023].
Because of overlapping specificities amongst SH2 domains, it is unlikely to be clear which proteins bind to a new pTyr candidate SH2-binding motif. Therefore temporal and spatial colocalization should be evaluated and ultimately direct in-cell binding demonstrated as well as interaction affinities measured by in vitro binding assays. In addition, some motifs might be bound by multiple SH2s, for example as part of a sequential signaling process.
o 18 selected references:

o 8 GO-Terms:

o 20 Instances for LIG_SH2_SFK_2
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P15498 VAV1
172 181 EAEGDEIYEDLMRSEPVSMP TP 1 Homo sapiens (Human)
P15498 VAV1
158 167 VEEDEDLYDCVENEEAEGDE TP 1 Homo sapiens (Human)
179 186 ENMVEDCLYETVKEIKEVAA TP 3 Homo sapiens (Human)
161 168 QGLGMEGPYEVLKDSSSQEN TP 3 Homo sapiens (Human)
P07333 CSF1R
559 565 IESYEGNSYTFIDPTQLPYN TP 2 Homo sapiens (Human)
P18052 Ptpra
823 829 FCYKVVQEYIDAFSDYANFK TP 2 Mus musculus (House mouse)
P18433 PTPRA
796 802 FCYKVVQEYIDAFSDYANFK TP 3 Homo sapiens (Human)
Q90738 AFAP1
451 457 DPGALHYDYIDVEMTASVIQ TP 2 Gallus gallus (Chicken)
Q14289 PTK2B
400 408 CSIESDIYAEIPDETLRRPG TP 8 Homo sapiens (Human)
Q63767 Bcar1
760 766 SEGGWMEDYDYVHLQGKEEF TP 3 Rattus norvegicus (Norway rat)
P56945 BCAR1
662 668 SEGGWMEDYDYVHLQGKEEF TP 5 Homo sapiens (Human)
P05622 Pdgfrb
748 755 MSKDESIDYVPMLDMKGDIK TP 2 Mus musculus (House mouse)
749 756 MSKDESVDYVPMLDMKGDVK TP 2 Homo sapiens (Human)
579 585 SSDGHEYIYVDPMQLPYDST TP 5 Homo sapiens (Human)
P00533 EGFR
1090 1096 DTFLPVPEYINQSVPKRPAG TP 1 Homo sapiens (Human)
O35177 Nedd9
626 632 SERSWMDDYDYVHLQGKEEF TP 2 Mus musculus (House mouse)
322 328 HQEEEEPQYEEIPIYLELLP TP 12 Hamster polyomavirus
Q14118 DAG1
890 895 KGSRPKNMTPYRSPPPYVPP TP 4 Homo sapiens (Human)
P34152-3 Ptk2
395 404 SVSETDDYAEIIDEEDTYTM TP 8 Mus musculus (House mouse)
Q14511 NEDD9
627 633 SERSWMDDYDYVHLQGKEEF TP 2 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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