The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
Phosphotyrosine ligands bound by SH2 domains
Functional site description:
Src Homology 2 (SH2) domains recognize small motifs containing a phosphorylated Tyrosine residue. Additional specificity determinants are mainly found up to four positions after the pTyr. They are primarily found in metazoa and close unicellular relatives which have Receptor Tyrosine Kinases (RTKs) as well as soluble TKs such as Src and Abl. SH2 is the main binding domain for TK phosphorylation signalling events.
ELMs with same func. site: LIG_SH2_CRK  LIG_SH2_GRB2like  LIG_SH2_NCK_1  LIG_SH2_PTP2  LIG_SH2_SRC  LIG_SH2_STAP1  LIG_SH2_STAT3  LIG_SH2_STAT5  LIG_SH2_STAT6 
ELM Description:
NCK is a ubiquitously expressed adaptor protein that modulates actin cytoskeleton dynamics and contains three SH3 domains and one SH2 domain at its C-terminal end. The human NCK family has two members, NCK1 (Nckα) and NCK2 (Nckβ/GRB4). Though NCK1 and NCK2 exhibit some degree of partner specificity, they share the same mode of ligand binding (Frese,2006). The NCK SH2 domain belongs to the class IA family, containing an aromatic residue (Phe) at the βD5 position (Kaneko,2010). Phosphopeptide libraries show that NCK1/2 SH2 domains bind the (Y)[DEStav][^KRHgw][PVAtslme][denqstagpm] consensus motif in tyrosine-phosphorylated proteins, with the main preference being for Pro or Val in position +3 and acidic or polar residues in position +1 with respect to the pTyr (Songyang,1993, Huang,2008). Two mammalian pathogens, enteropathogenic Escherichia coli (EPEC) and vaccinia virus, exploit Nck as part of their infection strategy. The Tir protein of EPEC, the main causative agent of severe infant diarrhea binds NCK1 and NCK2 SH2 domains through a high-affinity pYDEV motif (Frese,2006). The phosphate group of Tyr is tightly bound in the conserved pTyr SH2 hydrophilic pocket. The other two positions important for binding are pY+3 and pY+1. In the NCK SH2 domain, 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. While Val is critical for the high-affinity interaction, other residues like Pro, Ala, and Ile are tolerated at pY+3 but cause a significant reduction in binding affinity. The pY+1 position strongly favours an Asp that makes a salt bridge with an Arg at the β D3 position, with Glu, Ser and Thr allowed. The residue at pY+2 is less important as it does not make direct side-chain interactions with the SH2 domain, but aromatic residues are not allowed. A large range of residues are tolerated at position pY+4 with the best binders being Ala, Thr, Ser, and Tyr. Position pY+6 favors negatively charged residues such as Asp and Glu.
Pattern: (Y)[DESTNA][^GWFY][VPAI][DENQSTAGYFP]
Pattern Probability: 0.0008293
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.
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
Q13094 LCP2
LCP2_HUMAN
145 149 PVEDDADYEPPPSNDEEALQ TP 3 Homo sapiens (Human)
Q13094 LCP2
LCP2_HUMAN
128 132 DGEDDGDYESPNEEEEAPVE TP 3 Homo sapiens (Human)
Q13094 LCP2
LCP2_HUMAN
113 117 SSFEEDDYESPNDDQDGEDD TP 3 Homo sapiens (Human)
P17948 FLT1
VGFR1_HUMAN
1333 1337 ACCSPPPDYNSVVLYSTPPI TP 2 Homo sapiens (Human)
Q99704 DOK1
DOK1_HUMAN
362 366 DPKEDPIYDEPEGLAPVPPQ TP 2 Homo sapiens (Human)
P68619 VACWR159
A36_VACCW
112 116 APSTEHIYDSVAGSTLLINN TP 3 Vaccinia virus WR
2 
B7UM99 tir
TIR_ECO27
474 478 HQPEEHIYDEVAADPGYSVI TP 6 Escherichia coli O127:H6 str. E2348/69
4 
P14317 HCLS1
HCLS1_HUMAN
378 382 EPEPENDYEDVEEMDRHEQE TP 4 Homo sapiens (Human)
1 
Q14247 CTTN
SRC8_HUMAN
421 425 RLPSSPVYEDAASFKAELSY TP 4 Homo sapiens (Human)
1 
Q9NP31 SH2D2A
SH22A_HUMAN
280 284 PKPSNPIYNEPDEPIAFYAM TP 4 Homo sapiens (Human)
1 
Q9Z2B5 Eif2ak3
E2AK3_MOUSE
561 565 QCQTESKYDSVSADVSDNSW TP 4 Mus musculus (House mouse)
1 
P52799 EFNB2
EFNB2_HUMAN
304 308 DSVFCPHYEKVSGDYGHPVY TP 1 Homo sapiens (Human)
1 
Q9QZS7-2 Nphs1
NPHN_MOUSE
1218 1222 YEDPRGIYDQVAADMDAGEP TP 4 Mus musculus (House mouse)
2 
Q9QZS7-2 Nphs1
NPHN_MOUSE
1194 1198 PGVWGPLYDEVQMDPYDLRW TP 4 Mus musculus (House mouse)
2 
Q9QZS7-2 Nphs1
NPHN_MOUSE
1177 1181 MAFPGHLYDEVERVYGPPGV TP 4 Mus musculus (House mouse)
2 
P98172 EFNB1
EFNB1_HUMAN
317 321 ENNYCPHYEKVSGDYGHPVY TP 1 Homo sapiens (Human)
2 
P09619 PDGFRB
PGFRB_HUMAN
1009 1013 LDTSSVLYTAVQPNEGDNDY TP 1 Homo sapiens (Human)
2 
Please cite: The eukaryotic linear motif resource - 2018 update. (PMID:29136216)

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