1hcs Citations

Solution structure of the human pp60c-src SH2 domain complexed with a phosphorylated tyrosine pentapeptide.

Biochemistry 34 2107-21 (1995)
Cited: 41 times
EuropePMC logo PMID: 7532003


Human pp60c-src is a cellular nonreceptor tyrosine kinase that participates in cytosolic signal transduction and has been implicated in the development of malignant tumors in the human breast and colon. Signal transduction is mediated by highly specific interactions between the SH2 domain and receptor phosphorylated tyrosine binding motifs. To elucidate the molecular conformation and interactions in solution, a family of highly resolved nuclear magnetic resonance (NMR) structures was determined for the src SH2 domain complexed with a high-affinity phosphorylated pentapeptide, acetyl-p YEEIE-OH. The 23 structures, generated with a distance geometry (DG) and a dynamical simulated annealing (SA) procedure, satisfied 2072 experimental restraints derived from a variety of multifrequency/multidimensional and isotope-filtered NMR data. Superimposition of residues 143-245 upon the mean coordinate set yielded an atomic rmsd of 0.58 +/- 0.09 A for the N, C alpha, C' atoms and 1.04 +/- 0.08 for all the non-hydrogen atoms. Residues in the ordered secondary structure regions superimpose to 0.29 +/- 0.04 A for the N, C alpha, C' and 0.73 +/- 0.08 A for all the non-hydrogen atoms. The angular order parameter calculated for the phi, psi angles was > 0.9 for 81 of the 106 protein residues. The main protein conformational features are three antiparallel beta-strands that traverse a compact core with an alpha-helix on each side of the core near the N- and C-termini. The observed intermolecular nuclear Overhauser effects (NOE) from the pY, +1E, and +3I residues positioned the ligand in an extended conformation across the SH2 domain surface with the pY and +3I side chains inserted into the protein binding pockets. In general, the protein conformation is consistent with previously reported structures of different SH2 domain complexes determined by X-ray crystallography. However, inter- or intramolecular interactions involving the guanidinium side chains of the solvated R alpha A2 or the buried R beta B5 were not observed at pH = 5.5 or 7.0. If such interactions exist in solution, the absence of any confirming data probably arises from rapid exchange with solvent and/or undetermined dynamic components. Thus, the unrestrained R alpha A2 side chain did not show an amino-aromatic interaction or a hydrogen bond to the -1 carbonyl oxygen as observed in the crystal structures. This result is consistent with the solution structure of a different SH2 domain complex. A more detailed comparison between the crystal structure and the NMR-derived solution structures of the same src SH2 domain complex is presented.(ABSTRACT TRUNCATED AT 400 WORDS)

Reviews citing this publication (4)

  1. Host-defence peptides of Australian anurans: structure, mechanism of action and evolutionary significance. Apponyi MA, Pukala TL, Brinkworth CS, Maselli VM, Bowie JH, Tyler MJ, Booker GW, Wallace JC, Carver JA, Separovic F, Doyle J, Llewellyn LE. Peptides 25 1035-1054 (2004)
  2. Glycosylated and phosphorylated proteins--expression in yeast and oocytes of Xenopus: prospects and challenges--relevance to expression of thermostable proteins. Li P, Gao XG, Arellano RO, Renugopalakrishnan V. Protein Expr. Purif. 22 369-380 (2001)
  3. Modular peptide recognition domains in eukaryotic signaling. Kuriyan J, Cowburn D. Annu Rev Biophys Biomol Struct 26 259-288 (1997)
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Articles citing this publication (37)

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  2. The antibiotic and anticancer active aurein peptides from the Australian Bell Frogs Litoria aurea and Litoria raniformis the solution structure of aurein 1.2. Rozek T, Wegener KL, Bowie JH, Olver IN, Carver JA, Wallace JC, Tyler MJ. Eur. J. Biochem. 267 5330-5341 (2000)
  3. Structure of a regulatory complex involving the Abl SH3 domain, the Crk SH2 domain, and a Crk-derived phosphopeptide. Donaldson LW, Gish G, Pawson T, Kay LE, Forman-Kay JD. Proc. Natl. Acad. Sci. U.S.A. 99 14053-14058 (2002)
  4. Maculatin 1.1, an anti-microbial peptide from the Australian tree frog, Litoria genimaculata solution structure and biological activity. Chia BC, Carver JA, Mulhern TD, Bowie JH. Eur. J. Biochem. 267 1894-1908 (2000)
  5. A new high affinity binding site for suppressor of cytokine signaling-3 on the erythropoietin receptor. Hörtner M, Nielsch U, Mayr LM, Heinrich PC, Haan S. Eur. J. Biochem. 269 2516-2526 (2002)
  6. Host defence peptides from the skin glands of the Australian blue mountains tree-frog Litoria citropa. Solution structure of the antibacterial peptide citropin 1.1. Wegener KL, Wabnitz PA, Carver JA, Bowie JH, Chia BC, Wallace JC, Tyler MJ. Eur. J. Biochem. 265 627-637 (1999)
  7. nNOS inhibition, antimicrobial and anticancer activity of the amphibian skin peptide, citropin 1.1 and synthetic modifications. The solution structure of a modified citropin 1.1. Doyle J, Brinkworth CS, Wegener KL, Carver JA, Llewellyn LE, Olver IN, Bowie JH, Wabnitz PA, Tyler MJ. Eur. J. Biochem. 270 1141-1153 (2003)
  8. Solution structure of the C-terminal SH2 domain of the human tyrosine kinase Syk complexed with a phosphotyrosine pentapeptide. Narula SS, Yuan RW, Adams SE, Green OM, Green J, Philips TB, Zydowsky LD, Botfield MC, Hatada M, Laird ER. Structure 3 1061-1073 (1995)
  9. Structure of a specific peptide complex of the carboxy-terminal SH2 domain from the p85 alpha subunit of phosphatidylinositol 3-kinase. Breeze AL, Kara BV, Barratt DG, Anderson M, Smith JC, Luke RW, Best JR, Cartlidge SA. EMBO J. 15 3579-3589 (1996)
  10. Conformationally constrained peptidomimetic inhibitors of signal transducer and activator of transcription. 3: Evaluation and molecular modeling. Mandal PK, Limbrick D, Coleman DR, Dyer GA, Ren Z, Birtwistle JS, Xiong C, Chen X, Briggs JM, McMurray JS. J. Med. Chem. 52 2429-2442 (2009)
  11. How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Zhou Y, Abagyan R. Fold Des 3 513-522 (1998)
  12. Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization. Henriques DA, Ladbury JE, Jackson RM. Protein Sci. 9 1975-1985 (2000)
  13. The SH2 domain from the tyrosine kinase Fyn in complex with a phosphotyrosyl peptide reveals insights into domain stability and binding specificity. Mulhern TD, Shaw GL, Morton CJ, Day AJ, Campbell ID. Structure 5 1313-1323 (1997)
  14. Structural basis for the binding of high affinity phosphopeptides to Stat3. McMurray JS. Biopolymers 90 69-79 (2008)
  15. Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding. Ward JM, Gorenstein NM, Tian J, Martin SF, Post CB. J. Am. Chem. Soc. 132 11058-11070 (2010)
  16. Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains. Sheinerman FB, Al-Lazikani B, Honig B. J. Mol. Biol. 334 823-841 (2003)
  17. The solution structure of uperin 3.6, an antibiotic peptide from the granular dorsal glands of the Australian toadlet, Uperoleia mjobergii. Chia BC, Carver JA, Mulhern TD, Bowie JH. J. Pept. Res. 54 137-145 (1999)
  18. The solution structure of the cytokine-binding domain of the common beta-chain of the receptors for granulocyte-macrophage colony-stimulating factor, interleukin-3 and interleukin-5. Mulhern TD, Lopez AF, D'Andrea RJ, Gaunt C, Vandeleur L, Vadas MA, Booker GW, Bagley CJ. J. Mol. Biol. 297 989-1001 (2000)
  19. Inhibitors to the Src SH2 domain: a lesson in structure--thermodynamic correlation in drug design. Henriques DA, Ladbury JE. Arch. Biochem. Biophys. 390 158-168 (2001)
  20. pH titration studies of an SH2 domain-phosphopeptide complex: unusual histidine and phosphate pKa values. Singer AU, Forman-Kay JD. Protein Sci. 6 1910-1919 (1997)
  21. 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)
  22. Structure, dynamics, and binding thermodynamics of the v-Src SH2 domain: implications for drug design. Taylor JD, Ababou A, Fawaz RR, Hobbs CJ, Williams MA, Ladbury JE. Proteins 73 929-940 (2008)
  23. Design of peptidomimetic ligands for the pp60src SH2 domain. Plummer MS, Lunney EA, Para KS, Shahripour A, Stankovic CJ, Humblet C, Fergus JH, Marks JS, Herrera R, Hubbell S, Saltiel A, Sawyer TK. Bioorg. Med. Chem. 5 41-47 (1997)
  24. The formation of a covalent complex between a dipeptide ligand and the src SH2 domain. Alligood KJ, Charifson PS, Crosby R, Consler TG, Feldman PL, Gampe RT, Gilmer TM, Jordan SR, Milstead MW, Mohr C, Peel MR, Rocque W, Rodriguez M, Rusnak DW, Shewchuk LM, Sternbach DD. Bioorg. Med. Chem. Lett. 8 1189-1194 (1998)
  25. Surface movement in water of splendipherin, the aquatic male sex pheromone of the tree frog Litoria splendida. Perriman AW, Apponyi MA, Buntine MA, Jackway RJ, Rutland MW, White JW, Bowie JH. FEBS J. 275 3362-3374 (2008)
  26. The solution structures and activity of caerin 1.1 and caerin 1.4 in aqueous trifluoroethanol and dodecylphosphocholine micelles. Wegener KL, Carver JA, Bowie JH. Biopolymers 69 42-59 (2003)
  27. Solution and solid state conformation of the human EGF receptor transmembrane region. Rigby AC, Grant CW, Shaw GS. Biochim. Biophys. Acta 1371 241-253 (1998)
  28. Simultaneous binding of two peptidyl ligands by a SRC homology 2 domain. Zhang Y, Zhang J, Yuan C, Hard RL, Park IH, Li C, Bell C, Pei D. Biochemistry 50 7637-7646 (2011)
  29. The solution structure of frenatin 3, a neuronal nitric oxide synthase inhibitor from the giant tree frog, Litoria infrafrenata. Brinkworth CS, Carver JA, Wegener KL, Doyle J, Llewellyn LE, Bowie JH. Biopolymers 70 424-434 (2003)
  30. Comparison of Composer and ORCHESTRAR. Dolan MA, Keil M, Baker DS. Proteins 72 1243-1258 (2008)
  31. Conformational determinants of phosphotyrosine peptides complexed with the Src SH2 domain. Nachman J, Gish G, Virag C, Pawson T, Pomès R, Pai E. PLoS ONE 5 e11215 (2010)
  32. The Src SH2 domain interacts dynamically with the focal adhesion kinase binding site as demonstrated by paramagnetic NMR spectroscopy. Lindfors HE, Drijfhout JW, Ubbink M. IUBMB Life 64 538-544 (2012)
  33. Reconstitution of a native-like SH2 domain from disordered peptide fragments examined by multidimensional heteronuclear NMR. Ojennus DD, Fleissner MR, Wuttke DS. Protein Sci. 10 2162-2175 (2001)
  34. Structure-activity studies of phosphorylated peptide inhibitors of the association of phosphatidylinositol 3-kinase with PDGF-beta receptor. Ramalingam K, Eaton SR, Cody WL, Lu GH, Panek RL, Waite LA, Decker SJ, Keiser JA, Doherty AM. Bioorg. Med. Chem. 3 1263-1272 (1995)
  35. A novel conserved phosphotyrosine motif in the Drosophila fibroblast growth factor signaling adaptor Dof with a redundant role in signal transmission. Csiszar A, Vogelsang E, Beug H, Leptin M. Mol. Cell. Biol. 30 2017-2027 (2010)
  36. Spectroscopic characterization of the SH2- and active site-directed peptide sequences of a bivalent Src kinase inhibitor. Desamero RZ, Kang J, Dol C, Chinwong J, Walters K, Sivarajah T, Profit AA. Appl Spectrosc 63 767-774 (2009)
  37. Electrostatic interactions in the reconstitution of an SH2 domain from constituent peptide fragments. Ojennus DD, Lehto SE, Wuttke DS. Protein Sci. 12 44-55 (2003)

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  1. Peptide Inhibitors of Src SH3-Sh2(Slash)Phosphoprotein Interactions. Gilmer T, Rodriguez M, Jordan S, Crosby R, Alligood K, Green M, Kimery M, Wagner C, Kinder D, Charifson P, Hassell AM, Willard D, Luther M, Rusnak D, Sternbach DD, Mehrotra M, Peel M, Shampine L, Davis R, Robbins J, Patel IR, Kassel D, Burkhart W, Moyer M, Bradshaw T, Berman J J. Biol. Chem. 269 31711- (1994)
  2. Nuclear Magnetic Resonance Structure of an Sh2 Domain of Phospholipase C-Gamma1 Complexed with a High Affinity Binding Peptide. Pascal SM, Singer AU, Gish G, Yamazaki T, Shoelson SE, Pawson T, Kay LE, Forman-Kay JD Cell 77 461- (1994)
  3. Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms. Waksman G, Shoelson SE, Pant N, Cowburn D, Kuriyan J Cell 72 779- (1993)
  4. Recognition of a High-Affinity Phosphotyrosyl Peptide by the Src Homology-2 Domain of P56Lck. Eck MJ, Shoelson SE, Harrison SC Nature 362 87- (1993)
  5. Human Cellular Src Gene: Nucleotide Sequence and Derived Amino Acid Sequence of the Region Coding for the Carboxy-Terminal Two-Thirds of Pp60C-Src. Anderson SK, Gibbs CP, Tanaka A, Kung HJ, Fugita DJ Mol. Cell. Biol. 5 1122- (1985)