Specificity of SH2 Domains

The specificity profile of individual SH2 domains was determined in a series of studies employing degenerate phosphopeptide library screens [53, 98] from which two consensus motifs emerged for SH2 domain binding [52-55,99,100]. One group of SH2 domains preferentially binds to a pTyr-Glu-Glu-Ile motif that defines a generic recognition sequence  

Xaa being hydrophilic and/or negatively charged, and Yaa being bulky and hydrophobic. 

The second group of SH2 domain proteins discriminates less and selects mainly hydrophobic residues with a consensus sequence  

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Gan W, Roux B (2009) Binding specificity of SH2 domains insight from free energy simulations. Proteins 74 996-1007... 

The binding specificity of SH2 domains is largely determined by residues C-termlnal to the phosphotyrosine in a target peptide. In contrast, the binding specificity of PTB domains is determined by specific residues five to eight residues N-terminal to a phosphotyrosine residue. Sometimes a PTB domain binds to a target peptide even if the tyrosine is not phosphorylated. 

While the interactions at the pTyr binding pocket are generally similar for all SH2 domains, those which involve residues other than pTyr are not. These interactions help to determine the specificity of SH2 domain-target recognition. Comparison of the many SH2 domain-phosphopeptide structures has revealed that different SH2 domains use somewhat different mechanisms to engage their respective targets. 

Information about the specificity of SH2 domain binding came initially from the structures of the Src and Lck SH2 domains in complex with tyrosyl phosphopeptides with the sequence Glu, Glu, He (EEI) C-ter-minal to the pTyr (pY) (Eck et al., 1993 Waksman et al., 1993). This pYEEI sequence had previously been identified to be specific for the Src family of SH2 domains, which includes Lck (see Section III). The Src and Lck structures are very similar to one another. Although the peptides employed in both studies contained residues outside the pYEEI motif, the structures indicate that only these four residues contact the SH2 domain. The peptide binds the SH2 domains perpendicular to the central p-sheet in an extended conformation (Fig. 2A). The pTyr makes contacts very similar to those observed for the structure of the Src SH2 domain in complex with low-affinity tyrosyl phosphopeptides (see above). However, in addition, the EEI motif makes specific contact with other residues of the protein. 

For the most part, the specificity of SH2 domain binding is determined by the residues of the target G-terminal to the pTyr. However, for some SH2 domains, the residues N-terminal to the pTyr can be important. For example, it has been determined that the N-SHP-2 SH2 domain has a requirement for a hydrophobic residue (Val, He, or Leu) at the position —2 to the pTyr (Burshtyn et al., 1997 Huyer et al., 1995). This unusual... 

The potential binding sites for various SH2 domain proteins on cytoplasmic receptor domains as well as on soluble proteins have been precisely mapped for several pTyr-containing target proteins. Apart from the impressive diversity of SH2 domain function, the fundamental property of all SH2 domains refers to the specific recognition of pTyr epitopes. 

The subcellular localization of protein tyrosine phosphatases is an important aspect of their function. The sequences of cytoplasmic protein tyrosine phosphatases frequently demonstrate sequence signals specifying a particular subcellular localization. This ensures that protein tyrosine phosphatases are only active at defined subcellular sites. The presence of SH2 domains in cytoplasmic protein tyrosine phosphatases also shows that these are coupled, via SH2-phosphotyrosine interactions, to specific substrates, where they then perform their actual function. 

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