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:
NCK is a major adaptor protein involved in membrane receptor signalling and modulation of actin cytoskeleton dynamics. It contains three SH3 domains and one SH2 domain at its C-terminal end. The human NCK1 (Nckα) and NCK2 (Nckβ/GRB4) SH2 domains show a degree of partner specificity but share the same mode of ligand binding (Frese,2006) and belong to the class IA family which contains an aromatic residue (Phe) at the specificity-determining βD5 position (Kaneko,2010). Phosphopeptide libraries show that NCK SH2 binds to the (Y)[DEStav][^KRHgw][PVAtslme][denqstagpm] consensus tyrosine-phosphorylated motif (Songyang,1993; Huang,2008). At least two mammalian pathogens, enteropathogenic Escherichia coli (EPEC) and vaccinia virus, exploit NCK as part of their infection strategy. The Tir protein of EPEC binds NCK1/NCK2 SH2 domains through a high affinity pYDEV motif (Frese,2006). The phosphate group of Tyr is tightly bound in the conserved pTyr binding pocket. The other two positions important for binding are pY+3 and pY+1. In NCK SH2 domains, the EF loop is positioned away from the BG loop, exposing the pY+3 binding pocket where the side chain of Val forms tight interactions. Val and Pro confer high-affinity binding at pY+3 - Ala and Ile are tolerated but confer weaker binding. Negatively charged residues Asp and Glu are favoured at pY+1, making a salt bridge with an Arg at the βD3 position. Ser, Thr, Asn and Ala are tolerated but confer weaker binding. Inspection of known binders reveals that weak residues are tolerated at pY+3 when pY+1 is strong and vice-versa, but are not tolerated at both positions. The residue at pY+2 does not make direct side chain interactions with the SH2 domain, but aromatic residues are not allowed. Position pY+4 is highly permissive favouring Ala, Thr, Ser and Tyr, and pY+6 favours negatively charged residues. Positively charged residues are disfavoured at pY-1 and pY-2 due to the positively charged SH2 domain surface, but are tolerated when pY+1 and pY+3 are strong residues.
Pattern Probability: 0.0003339
Present in taxon: Metazoa
Interaction Domain:
SH2 (PF00017) SH2 domain (Stochiometry: 1 : 1)
o See 17 Instances for LIG_SH2_NCK_1
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 6 selected references:

o 15 GO-Terms:

o 17 Instances for LIG_SH2_NCK_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
B7UM99 tir
472 478 AHQPEEHIYDEVAADPGYSV TP 6 Escherichia coli O127:H6 str. E2348/69
1007 1013 PLDTSSVLYTAVQPNEGDND TP 1 Homo sapiens (Human)
P98172 EFNB1
315 321 TENNYCPHYEKVSGDYGHPV TP 1 Homo sapiens (Human)
Q9QZS7-2 Nphs1
1175 1181 DMAFPGHLYDEVERVYGPPG TP 4 Mus musculus (House mouse)
Q9QZS7-2 Nphs1
1192 1198 PPGVWGPLYDEVQMDPYDLR TP 4 Mus musculus (House mouse)
Q9QZS7-2 Nphs1
1216 1222 KYEDPRGIYDQVAADMDAGE TP 4 Mus musculus (House mouse)
P52799 EFNB2
302 308 ADSVFCPHYEKVSGDYGHPV TP 1 Homo sapiens (Human)
Q9Z2B5 Eif2ak3
559 565 TQCQTESKYDSVSADVSDNS TP 4 Mus musculus (House mouse)
278 284 RPKPSNPIYNEPDEPIAFYA TP 4 Homo sapiens (Human)
Q14247 CTTN
419 425 ERLPSSPVYEDAASFKAELS TP 4 Homo sapiens (Human)
P14317 HCLS1
376 382 PEPEPENDYEDVEEMDRHEQ TP 4 Homo sapiens (Human)
P68619 VACWR159
110 116 MAPSTEHIYDSVAGSTLLIN TP 3 Vaccinia virus WR
Q99704 DOK1
360 366 TDPKEDPIYDEPEGLAPVPP TP 2 Homo sapiens (Human)
P17948 FLT1
1331 1337 ACCSPPPDYNSVVLYSTPPI TP 2 Homo sapiens (Human)
Q13094 LCP2
111 117 WSSFEEDDYESPNDDQDGED TP 3 Homo sapiens (Human)
Q13094 LCP2
126 132 QDGEDDGDYESPNEEEEAPV TP 3 Homo sapiens (Human)
Q13094 LCP2
143 149 APVEDDADYEPPPSNDEEAL TP 3 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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