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_PTP2  LIG_SH2_SRC  LIG_SH2_STAT3  LIG_SH2_STAT5  LIG_SH2_STAT6 
ELM Description:
The SH2 domain of the CRK family (CRK-1, CRK-II splice isoforms and CRK-like) binds a phosphotyrosine motif with optimal specificity for Pro or Leu at the pY+3 position (Liu,2010; Huang,2008; 1JU5). The motif appears to be present in pre-metazoans as well as in metazoans (Shigeno-Nakazawa,2016). The SH2 domain topology consists of a central β sheet with three anti-parallel β strands and two α helices, one each side of the sheet (Donaldson,2002). The pY residue of the ligand interacts with two highly conserved basic residues (R15 and R33) in the phosphotyrosine binding pocket situated at one side of the anti-parallel β sheet. Pro at the pY+3 position is buried in a hydrophobic pocket that lies on the other side of the three anti-parallel beta sheets. This hydrophobic pocket is lined by residues Y60, I61, I89, and L109 from the EF and BG loops that make important non-polar contacts with the pY+3 residue. The intermediate residue positions are more tolerant, indicating they are less critical for the interaction. However; peptide library SPOT arrays reveal residue preferences at specific positions which significantly diminish or even prohibit binding (Liu,2010; Huang,2008). Arrays also show that Val or Ile are allowed at +3, though they are clearly weaker than Pro or Leu and may require optimal residues in the adjacent positions to reach a good affinity.
Acidic residues are disfavored at multiple positions. Hydrophobic residues, particularly large ones, are disfavoured at several positions. Unusually for SH2, basic residues are tolerated in several positions, with His being less preferred. Pro is prohibited at the +1 position. As seen in some of the physiological ligands, an Arg residue is most favoured at the pY+4 position as it is positioned to contact Asp-91 in the CRK SH2 domain (1JU5) whereas acidic residues are non-permissive (Liu,2010; Huang,2008). The current pattern is predominantly derived from the SPOT arrays for CRK and CRKL in (Huang,2008)
Pattern: (Y)[^EPILVFYW][^HDEW][PLIV][^DEW]
Pattern Probability: 0.0015153
Present in taxons: Choanoflagellida Metazoa
Interaction Domain:
SH2 (PF00017) SH2 domain (Stochiometry: 1 : 1)
o See 34 Instances for LIG_SH2_CRK
o Abstract
The Src Homology 2 (SH2) domain is a major protein interaction module that is central to tyrosine kinase signalling. 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 signalling 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 signalling process.
o 7 selected references:

o 11 GO-Terms:

o 34 Instances for LIG_SH2_CRK
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P09619 PDGFRB
PGFRB_HUMAN
771 775 ADIESSNYMAPYDNYVPSAP FP 4 Homo sapiens (Human) [new]
1 
P16234 PDGFRA
PGFRA_HUMAN
762 766 SDIQRSLYDRPASYKKKSML FP 4 Homo sapiens (Human) [new]
1 
Q01973 ROR1
ROR1_HUMAN
789 793 SNPRYPNYMFPSQGITPQGQ TP 1 Homo sapiens (Human) [new]
1 
O15197 EPHB6
EPHB6_HUMAN
635 639 YTEQLQQYSSPGLGVKYYID TP 1 Homo sapiens (Human) [new]
1 
P46108 CRK
CRK_HUMAN
221 225 GGPEPGPYAQPSVNTPLPNL TP 1 Homo sapiens (Human) [new]
1 
P19174 PLCG1
PLCG1_HUMAN
1253 1257 EGSFESRYQQPFEDFRISQE FP 1 Homo sapiens (Human) [new]
1 
P49023 PXN
PAXI_HUMAN
118 122 VGEEEHVYSFPNKQKSAEPS TP 1 Homo sapiens (Human) [new]
1 
Q61140 Bcar1
BCAR1_MOUSE
376 380 PPPAPDLYDVPPGLRRPGPG TP 1 Mus musculus (House mouse) [new]
1 
Q61140 Bcar1
BCAR1_MOUSE
310 314 SSSHHSVYDVPPSVSKDVPD TP 1 Mus musculus (House mouse) [new]
1 
Q61140 Bcar1
BCAR1_MOUSE
291 295 RDPLLDVYDVPPSVEKGLLS TP 1 Mus musculus (House mouse) [new]
1 
Q61140 Bcar1
BCAR1_MOUSE
271 275 NQYGQEVYDTPPMAVKGPNG TP 1 Mus musculus (House mouse) [new]
1 
Q61140 Bcar1
BCAR1_MOUSE
238 242 AQTEQDEYDTPRHLLAPGPQ TP 1 Mus musculus (House mouse) [new]
1 
Q61140 Bcar1
BCAR1_MOUSE
169 173 PSPATDLYQVPPGPGSPAQD TP 1 Mus musculus (House mouse) [new]
1 
Q18PE0 Dok7
DOK7_MOUSE
406 410 PTSLRHHYDTPRSLRQAPRD TP 1 Mus musculus (House mouse) [new]
1 
Q18PE0 Dok7
DOK7_MOUSE
396 400 CPPGAAEYQVPTSLRHHYDT TP 1 Mus musculus (House mouse) [new]
1 
P56945 BCAR1
BCAR1_HUMAN
362 366 SPPAEDVYDVPPPAPDLYDV TP 2 Homo sapiens (Human) [new]
1 
P47817 wee2-a
WEE2A_XENLA
403 407 NEILQEDYSQLPKADIFALG FP 4 Xenopus laevis (African clawed frog) [new]
1 
P47817 wee2-a
WEE2A_XENLA
110 114 YTPKSLLYKTLPSPGSRVHC TP 4 Xenopus laevis (African clawed frog) [new]
1 
P97318 Dab1
DAB1_MOUSE
232 236 SQKKEGVYDVPKSQPNSQPL TP 3 Mus musculus (House mouse) [new]
1 
P97318 Dab1
DAB1_MOUSE
220 224 PETEENIYQVPTSQKKEGVY TP 3 Mus musculus (House mouse) [new]
1 
Q13191 CBLB
CBLB_HUMAN
709 713 VEEDDDEYKIPSSHPVSLNS TP 2 Homo sapiens (Human) [new]
1 
Q13191 CBLB
CBLB_HUMAN
665 669 GHLGSEEYDVPPRLSPPPPV TP 2 Homo sapiens (Human) [new]
1 
P08069 IGF1R
IGF1R_HUMAN
973 977 RLGNGVLYASVNPEYFSAAD FP 3 Homo sapiens (Human) [new]
1 
Q8N8Z6 DCBLD1
DCBD1_HUMAN
696 700 HPGTSDSYSAPRDCLTPLNQ TP 3 Homo sapiens (Human) [new]
1 
Q8N8Z6 DCBLD1
DCBD1_HUMAN
665 669 AQPADRGYDRPKAVSALATE TP 3 Homo sapiens (Human) [new]
1 
Q8N8Z6 DCBLD1
DCBD1_HUMAN
652 656 VGAQDGDYQRPHSAQPADRG TP 3 Homo sapiens (Human) [new]
1 
Q8N8Z6 DCBLD1
DCBD1_HUMAN
621 625 TFSAQSGYRVPGPQPGHKHS TP 3 Homo sapiens (Human) [new]
1 
Q8N8Z6 DCBLD1
DCBD1_HUMAN
589 593 QRAGRHEYALPLAPPEPEYA TP 3 Homo sapiens (Human) [new]
1 
Q8N8Z6 DCBLD1
DCBD1_HUMAN
578 582 STDAGGHYDCPQRAGRHEYA TP 3 Homo sapiens (Human) [new]
1 
Q8N8Z6 DCBLD1
DCBD1_HUMAN
540 544 ITSDMADYQQPLMIGTGTVT FP 3 Homo sapiens (Human) [new]
1 
Q64010 Crk
CRK_MOUSE
221 225 GGPEPGPYAQPSVNTPLPNL TP 1 Mus musculus (House mouse) [new]
1 
P22681 CBL
CBL_HUMAN
774 778 SENEDDGYDVPKPPVPAVLA TP 3 Homo sapiens (Human) [new]
1 
P49024 PXN
PAXI_CHICK
31 35 FLTEETPYSYPTGNHTYQEI TP 3 Gallus gallus (Chicken) [new]
1 
P49024 PXN
PAXI_CHICK
118 122 ASEEEHVYSFPNKQKSAEPS TP 3 Gallus gallus (Chicken) [new]
1 
Please cite: The eukaryotic linear motif resource - 2018 update. (PMID:29136216)

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