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Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain.

Severin A, Joseph RE, Boyken S, Fulton DB, Andreotti AH
J Mol Biol 387 726-43 (2009)
Cited: 27 times
EuropePMC logo PMID: 19361414

Abstract

We report here the NMR-derived structure of the binary complex formed by the interleukin-2 tyrosine kinase (Itk) Src homology 3 (SH3) and Src homology 2 (SH2) domains. The interaction is independent of both a phosphotyrosine motif and a proline-rich sequence, the classical targets of the SH2 and SH3 domains, respectively. The Itk SH3/SH2 structure reveals the molecular details of this nonclassical interaction and provides a clear picture for how the previously described prolyl cis/trans isomerization present in the Itk SH2 domain mediates SH3 binding. The higher-affinity cis SH2 conformer is preorganized to form a hydrophobic interface with the SH3 domain. The structure also provides insight into how autophosphorylation in the Itk SH3 domain might increase the affinity of the intermolecular SH3/SH2 interaction. Finally, we can compare this Itk complex with other examples of SH3 and SH2 domains engaging their ligands in a nonclassical manner. These small binding domains exhibit a surprising level of diversity in their binding repertoires.

Articles - 2k7a mentioned but not cited (2)

  1. Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain. Severin A, Joseph RE, Boyken S, Fulton DB, Andreotti AH. J Mol Biol 387 726-743 (2009)
  2. CARDIO-PRED: an in silico tool for predicting cardiovascular-disorder associated proteins. Jain P, Thukral N, Gahlot LK, Hasija Y. Syst Synth Biol 9 55-66 (2015)


Reviews citing this publication (7)

  1. T-cell signaling regulated by the Tec family kinase, Itk. Andreotti AH, Schwartzberg PL, Joseph RE, Berg LJ. Cold Spring Harb Perspect Biol 2 a002287 (2010)
  2. The Src, Syk, and Tec family kinases: distinct types of molecular switches. Bradshaw JM. Cell Signal 22 1175-1184 (2010)
  3. Protein conformational switches: from nature to design. Ha JH, Loh SN. Chemistry 18 7984-7999 (2012)
  4. ITK inhibitors in inflammation and immune-mediated disorders. Sahu N, August A. Curr Top Med Chem 9 690-703 (2009)
  5. NMR reveals novel mechanisms of protein activity regulation. Kalodimos CG. Protein Sci 20 773-782 (2011)
  6. Regulation of Hematopoietic Cell Development and Function Through Phosphoinositides. Elich M, Sauer K. Front Immunol 9 931 (2018)
  7. Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities. Gurung D, Danielson JA, Tasnim A, Zhang JT, Zou Y, Liu JY. Biology (Basel) 12 1008 (2023)

Articles citing this publication (18)

  1. Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts. Shen Y, Bax A. J Biomol NMR 46 199-204 (2010)
  2. Loops govern SH2 domain specificity by controlling access to binding pockets. Kaneko T, Huang H, Zhao B, Li L, Liu H, Voss CK, Wu C, Schiller MR, Li SS. Sci Signal 3 ra34 (2010)
  3. Structural basis for regulation of the Crk signaling protein by a proline switch. Sarkar P, Saleh T, Tzeng SR, Birge RB, Kalodimos CG. Nat Chem Biol 7 51-57 (2011)
  4. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Kaneko T, Joshi R, Feller SM, Li SS. Cell Commun Signal 10 32 (2012)
  5. Domain organization differences explain Bcr-Abl's preference for CrkL over CrkII. Jankowski W, Saleh T, Pai MT, Sriram G, Birge RB, Kalodimos CG. Nat Chem Biol 8 590-596 (2012)
  6. Evolving specificity from variability for protein interaction domains. Kaneko T, Sidhu SS, Li SS. Trends Biochem Sci 36 183-190 (2011)
  7. Crystal structures of IL-2-inducible T cell kinase complexed with inhibitors: insights into rational drug design and activity regulation. Kutach AK, Villaseñor AG, Lam D, Belunis C, Janson C, Lok S, Hong LN, Liu CM, Deval J, Novak TJ, Barnett JW, Chu W, Shaw D, Kuglstatter A. Chem Biol Drug Des 76 154-163 (2010)
  8. Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav. Chen CH, Martin VA, Gorenstein NM, Geahlen RL, Post CB. Mol Cell Biol 31 2984-2996 (2011)
  9. Calmodulin and PI(3,4,5)P₃ cooperatively bind to the Itk pleckstrin homology domain to promote efficient calcium signaling and IL-17A production. Wang X, Boyken SE, Hu J, Xu X, Rimer RP, Shea MA, Shaw AS, Andreotti AH, Huang YH. Sci Signal 7 ra74 (2014)
  10. Disrupting the intermolecular self-association of Itk enhances T cell signaling. Min L, Wu W, Joseph RE, Fulton DB, Berg L, Andreotti AH. J Immunol 184 4228-4235 (2010)
  11. Crystal structure of Src-like adaptor protein 2 reveals close association of SH3 and SH2 domains through β-sheet formation. Wybenga-Groot LE, McGlade CJ. Cell Signal 25 2702-2708 (2013)
  12. In silico modeling of Itk activation kinetics in thymocytes suggests competing positive and negative IP4 mediated feedbacks increase robustness. Mukherjee S, Rigaud S, Seok SC, Fu G, Prochenka A, Dworkin M, Gascoigne NR, Vieland VJ, Sauer K, Das J. PLoS One 8 e73937 (2013)
  13. Rescue of the aggregation prone Itk Pleckstrin Homology domain by two mutations derived from the related kinases, Btk and Tec. Boyken SE, Fulton DB, Andreotti AH. Protein Sci 21 1288-1297 (2012)
  14. Demonstration of Binding Induced Structural Plasticity in a SH2 Domain. Visconti L, Toto A, Jarvis JA, Troilo F, Malagrinò F, De Simone A, Gianni S. Front Mol Biosci 7 89 (2020)
  15. Dynamics of the Tec-family tyrosine kinase SH3 domains. Roberts JM, Tarafdar S, Joseph RE, Andreotti AH, Smithgall TE, Engen JR, Wales TE. Protein Sci 25 852-864 (2016)
  16. Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures. Joseph RE, Ginder ND, Hoy JA, Nix JC, Fulton DB, Honzatko RB, Andreotti AH. Acta Crystallogr Sect F Struct Biol Cryst Commun 68 145-153 (2012)
  17. Structure and function of Tec family kinase Itk. Qi Q, Kannan AK, August A. Biomol Concepts 2 223-232 (2011)
  18. The HIV-1 protein Nef activates the Tec family kinase Btk by stabilizing an intermolecular SH3-SH2 domain interaction. Aryal M, Lin D, Regan K, Du S, Shi H, Alvarado JJ, Ilina TV, Andreotti AH, Smithgall TE. Sci Signal 15 eabn8359 (2022)


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