title: Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2.
abstract: Advances in mass spectrometry-based proteomics have yielded a substantial mapping of the tyrosine phosphoproteome and thus provided an important step toward a systematic analysis of intracellular signaling networks in higher eukaryotes. In this study we decomposed an uncharacterized proteomics data set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid binding.
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark.
authors.forename: Martin Lee
authors.initials: ML
authors.lastname: Miller
authors.forename: Stefan
authors.initials: S
authors.lastname: Hanke
authors.forename: Anders Mørkeberg
authors.initials: AM
authors.lastname: Hinsby
authors.forename: Carsten
authors.initials: C
authors.lastname: Friis
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.forename: Nikolaj
authors.initials: N
authors.lastname: Blom
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D016000:Cluster Analysis; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D000072181:Inositol Polyphosphate 5-Phosphatases; D008969:Molecular Sequence Data; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry*; D019000:Phosphotyrosine / Q000737:chemistry*; D010802:Phylogeny; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry*; D015203:Reproducibility of Results
chemical_list: D020543:Proteome; D019000:Phosphotyrosine; D010744:Phosphoric Monoester Hydrolases; D000072181:Inositol Polyphosphate 5-Phosphatases