Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 10 (1), 32

Phosphotyrosine Recognition Domains: The Typical, the Atypical and the Versatile

Affiliations

Phosphotyrosine Recognition Domains: The Typical, the Atypical and the Versatile

Tomonori Kaneko et al. Cell Commun Signal.

Abstract

SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCδ and PKCθ C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases.

Figures

Figure 1
Figure 1
Structure and sequence patterns of the SH2 domain. (A) Structure of the v-Src SH2 domain in complex with the pYEEI peptide (PDB ID: 1SPS). The two conserved α-helices are coloured green, and the seven β-strands are coloured orange. The peptide is shown as grey sticks. The phosphate group of pTyr binds to Arg175 located on the βB strand of the SH2 domain. The pTyr+3 Ile side chain is captured by a hydrophobic pocket provided between the EF and BG loops. (B) Conservation and variation in the secondary structural elements of SH2 domains based on experimentally determined structures. Refer to [40] for a list of SH2 domain structures. The N-terminal half of an SH2 domain is dedicated to pTyr recognition and is much less variable than the C-terminal half where the specificity pocket is located. A dashed line indicates that the element does not exist in an SH2 domain. Structural variations are observed more often in the C-terminal half. For example, the BG loop of the STAP family (BRDG1 & BKS) and the Cbl family SH2 domains are much shorter than in other SH2 domains, which results in an open pocket capable of binding a hydrophobic pTyr +4 residue [40,43]. Pro287 of the ITK SH2 domain is susceptible to cistrans isomerization via its CD loop, which leads to a switch of binding partners [44-46]. The long, proline-rich DE loop insertion in the Crk SH2 domain is the binding site for the Abl SH3 domain [47]. (C) The tandem SH2 domains of the transcription factor Spt6. Four research groups have reported crystal and solution structures, which are essentially identical to each other [48-51]. Shown here is the crystal structure of the Saccharomyces cerevisiae Spt6 with a sulfate ion located in the "canonical" phospho-residue binding pocket of the N-terminal SH2 domain (PDB ID: 3PSK) [48]. Mutagenesis studies and NMR titration analysis suggested that this pocket, involving Arg1282, as well as a positively charged patch, including Lys1435 of the C-terminal SH2 domain (residues shown as cyan sticks), are the binding sites of the phosphorylated CTD peptides [49,50,52].
Figure 2
Figure 2
Surface loops in the SH2 domain confer multiple binding modes to the tyrosine phosphatase SHP2. The N-terminal SH2 (N-SH2), C-terminal SH2 (C-SH2) and the phosphatase domains are coloured in light blue, orange, and cyan, respectively. The EF and BG loops of the N-SH2 domain are coloured brown and magenta, respectively. Molecular orientation is aligned for the N-SH2 domain, and drawn to scale. (A) The inhibitory state of SHP2 (PDB ID: 2SHP) [87]. The DE loop region of the N-SH2 domain, including the side chain of Asp61 (coloured red), mimics a pTyr substrate and blocks the active site of the phosphatase domain. In this conformation, the BG loop contacts the EF loop and inhibits ligand binding. (B) The 1:1 binding mode (PDB ID: 3TL0) [90]. The bound LNpYAQLW peptide is coloured yellow. The C-terminal region of the single peptide binds to a cleft between the EF and BG loops. (C) The 1:2 binding mode, in which the two identical peptides, with a sequence VIpYFVPL, form a short, antiparallel β-sheet and bind to a single SH2 domain (PDB ID: 3TKZ) [90]. The BG loop is positioned to accommodate the two peptides.
Figure 3
Figure 3
Binding partner switch induced by tyrosine phosphorylation. The sequence of the T-cell receptor subunit, CD3ε, contains two interaction motifs overlapping at a tyrosine phosphorylation site. The two phosphorylation sites Tyr166 and 177 are coloured red. The binding partners of the motifs, depending on the phosphorylation state, is schematically depicted as highlighted boxes.
Figure 4
Figure 4
Diversity in ligand recognition in the PTB domain family. PTB domains are shown in ribbon representations, with α-helices in green, and β-strands in orange. Bound peptides are drawn as gray sticks. (A) The PTB domain of IRS-1 bound to a pTyr-containing peptide derived from interleukin 4, containing an NPApY sequence (PDB ID: 1IRS) [105]. The two arginine residues, Arg212 and Arg227 (coloured blue), provide electrostatic contacts with pTyr at position 0 (coloured yellow). (B) The Numb PTB domain bound to an NAK-derived peptide (PDB ID: 1DDM) [111]. The peptide contains an NMSF sequence, but not a tyrosine. Phe149 and Phe195 (coloured magenta) of the PTB domain are essential for peptide binding. (C) The tensin2 PTB domain bound to a peptide derived from DLC-1 (PDB ID: 2LOZ) [112]. The peptide, which does not contain an NXX[Y/F] motif, binds to a novel site on the PTB domain that involves the α1 helix.
Figure 5
Figure 5
The structure and sequence conservation of the HYB domain. (A) The HYB domain is coordinated with six zinc ions. Shown is the homo-dimeric structure of the Hakai HYB domain (showing the two chains with different colours) (PDB ID: 3VK6) [96]. Zinc ions are depicted as spheres. The 24 residues (12 per monomer) coordinating the zinc ions are shown as green sticks. The four residues, His127, Tyr176, His185, and Arg189 from each monomer, identified as sticks, mainly contribute to pTyr binding by providing a positively charged pocket. (B) HYB domain-like sequences identified in animals and plants. The alignment was generated by the program MAFFT [130]. The 12 zinc-binding residues are shaded green, showing that all of them are strictly conserved within these species. The human Hakai HYB domain was aligned with following sequences with UniProt IDs: zebrafish (Q5RGV5), fruit fly (Q9VIT1), Arabidopsis thaliana (Q9LFC0), wine grape (F6HKX7), and Japanese rice (Q0IWQ6).
Figure 6
Figure 6
Atypical pTyr recognition proteins. On the left panels, molecular surface of each protein is overlaid on ribbon representation. (A) The C2 domain from the human PKCδ bound to a pTyr-peptide (PDB ID: 1YRK) [145]. The peptide is shown as grey sticks. Positively charged residues (green sticks) of the C2 domain that engage the pTyr moiety are shown to highlight the histidine-phenyl ring stacking feature. (B) pTyr binding by the human RKIP (PDB ID: 2QYQ) [149]. The structure features a deep pocket complementary to the pTyr side chain. The structure also highlights the lack of lysine and arginine in the binding pocket. (C) The homo-tetrameric active form of the human PKM2 bound to FBP (PDB ID: 3BJF) [150]. Each monomer is depicted with a different colour. The allosteric activator FBP is drawn as space-filling models. The distal active site from a monomer is identified with a blue circle. In the inset, the "lip" of the FBP-binding pocket created by the Lys433 and Trp482 residues and a loop region is coloured green. A pTyr ligand also binds to this region, and promotes the release of the FBP molecule, which results in inactivation of PKM2.
Figure 7
Figure 7
Mutations that confer PTP activity to catalytically-dead phosphatases. The catalytic signature motif sequences are extracted from the active phosphatases PTP1B and PTEN, along with five phosphatase-like domains. The His, Cys and Arg residues in the HCX5R motif, conserved among active PTP domains, are coloured red. The arrowhead indicates the catalytic cysteine. Mutations that have experimentally proven to restore catalytic activity are also indicated, for STYX [152], MK-STYX [157] and HD-PTP [159]. EGG4/5, Tensin1 and auxilin are predicted to be devoid of PTP activity owing to the lack of a signature motif residue [121,158].
Figure 8
Figure 8
Evolution of the human PTK signalling circuit. A schematic depicting the evolution of the human PTK circuit, where a, b, c, d, and e denote intracellular human circuits of a primitive origin, a, f, c, d, and e denote circuits with receptor tyrosine kinases and cytoplasmic substrates of bilaterian origin, and g, b, h, i and e denote vertebrate-origin circuits in which membrane-bound substrates are phosphorylated by cytoplasmic tyrosine kinases of a primitive origin in a tissue-specific manner. See reference [8] for more details.

Similar articles

See all similar articles

Cited by 16 PubMed Central articles

See all "Cited by" articles

References

    1. Seet BT, Dikic I, Zhou MM, Pawson T. Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol. 2006;7:473–483. - PubMed
    1. Lahiry P, Torkamani A, Schork NJ, Hegele RA. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet. 2010;11:60–74. doi: 10.1038/nrg2707. - DOI - PubMed
    1. Hunter T. Tyrosine phosphorylation: thirty years and counting. Curr Opin Cell Biol. 2009;21:140–146. doi: 10.1016/j.ceb.2009.01.028. - DOI - PMC - PubMed
    1. Jin J, Xie X, Chen C, Park JG, Stark C, James DA, Olhovsky M, Linding R, Mao Y, Pawson T. Eukaryotic protein domains as functional units of cellular evolution. Sci Signal. 2009;2:ra76. doi: 10.1126/scisignal.2000546. - DOI - PubMed
    1. Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science. 2003;300:445–452. doi: 10.1126/science.1083653. - DOI - PubMed
Feedback