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Structural characterization of Lyn-SH3 domain in complex with a herpesviral protein reveals an extended recognition motif that enhances binding affinity.

Bauer F, Schweimer K, Meiselbach H, Hoffmann S, Rösch P, Sticht H
Protein Sci 14 2487-98 (2005)
Cited: 39 times
EuropePMC logo PMID: 16155203

Abstract

The Src homology 3 (SH3) domain of the Src family kinase Lyn binds to the herpesviral tyrosine kinase interacting protein (Tip) more than one order of magnitude stronger than other closely related members of the Src family. In order to identify the molecular basis for high-affinity binding, the structure of free and Tip-bound Lyn-SH3 was determined by NMR spectroscopy. Tip forms additional contacts outside its classical proline-rich recognition motif and, in particular, a strictly conserved leucine (L186) of the C-terminally adjacent sequence stretch packs into a hydrophobic pocket on the Lyn surface. Although the existence of this pocket is no unique property of Lyn-SH3, Lyn is the only Src family kinase that contains an additional aromatic residue (H41) in the n-Src loop as part of this pocket. H41 covers L186 of Tip by forming tight hydrophobic contacts, and model calculations suggest that the increase in binding affinity compared with other SH3 domains can mainly be attributed to these additional interactions. These findings indicate that this pocket can mediate specificity even between otherwise closely related SH3 domains.

Articles - 1w1f mentioned but not cited (9)

  1. Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models. Hou T, Li N, Li Y, Wang W. J. Proteome Res. 11 2982-2995 (2012)
  2. Structural characterization of Lyn-SH3 domain in complex with a herpesviral protein reveals an extended recognition motif that enhances binding affinity. Bauer F, Schweimer K, Meiselbach H, Hoffmann S, Rösch P, Sticht H. Protein Sci. 14 2487-2498 (2005)
  3. Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry. Engen JR, Wales TE, Chen S, Marzluff EM, Hassell KM, Weis DD, Smithgall TE. Int Rev Phys Chem 32 96-127 (2013)
  4. Potent and selective inhibition of SH3 domains with dirhodium metalloinhibitors. Vohidov F, Knudsen SE, Leonard PG, Ohata J, Wheadon MJ, Popp BV, Ladbury JE, Ball ZT. Chem Sci 6 4778-4783 (2015)
  5. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors. Zafra Ruano A, Cilia E, Couceiro JR, Ruiz Sanz J, Schymkowitz J, Rousseau F, Luque I, Lenaerts T. PLoS Comput. Biol. 12 e1004938 (2016)
  6. Aminoquinoline-Rhodium(II) Conjugates as Src-Family SH3 Ligands. Martin SC, Ball ZT. ACS Med Chem Lett 10 1380-1385 (2019)
  7. The Two Isoforms of Lyn Display Different Intramolecular Fuzzy Complexes with the SH3 Domain. Teixeira JMC, Fuentes H, Bielskutė S, Gairi M, Żerko S, Koźmiński W, Pons M. Molecules 23 (2018)
  8. Computational evaluation of anticipated PE_PGRS39 protein involvement in host-pathogen interplay and its integration into vaccine development. Patni K, Agarwal P, Kumar A, Meena LS. 3 Biotech 11 204 (2021)
  9. Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding. Tőke O, Koprivanacz K, Radnai L, Merő B, Juhász T, Liliom K, Buday L. Cells 10 173 (2021)


Reviews citing this publication (2)

  1. The emerging contribution of sequence context to the specificity of protein interactions mediated by PDZ domains. Luck K, Charbonnier S, Travé G. FEBS Lett. 586 2648-2661 (2012)
  2. SH3 domains: modules of protein-protein interactions. Kurochkina N, Guha U. Biophys Rev 5 29-39 (2013)

Articles citing this publication (28)

  1. Partial unfolding of diverse SH3 domains on a wide timescale. Wales TE, Engen JR. J. Mol. Biol. 357 1592-1604 (2006)
  2. Crystal structure analysis and solution studies of human Lck-SH3; zinc-induced homodimerization competes with the binding of proline-rich motifs. Romir J, Lilie H, Egerer-Sieber C, Bauer F, Sticht H, Muller YA. J. Mol. Biol. 365 1417-1428 (2007)
  3. Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domains. Zhou HX. Biophys. J. 91 3170-3181 (2006)
  4. Recognition of non-canonical peptides by the yeast Fus1p SH3 domain: elucidation of a common mechanism for diverse SH3 domain specificities. Kim J, Lee CD, Rath A, Davidson AR. J. Mol. Biol. 377 889-901 (2008)
  5. Solution structure of a Hck SH3 domain ligand complex reveals novel interaction modes. Schmidt H, Hoffmann S, Tran T, Stoldt M, Stangler T, Wiesehan K, Willbold D. J. Mol. Biol. 365 1517-1532 (2007)
  6. Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1. Yan C, Kaoud T, Lee S, Dalby KN, Ren P. J Phys Chem B 115 1491-1502 (2011)
  7. Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: loop flexibility and amyloid aggregation. Martín-García JM, Luque I, Mateo PL, Ruiz-Sanz J, Cámara-Artigas A. FEBS Lett. 581 1701-1706 (2007)
  8. Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p. Stollar EJ, Garcia B, Chong PA, Rath A, Lin H, Forman-Kay JD, Davidson AR. J. Biol. Chem. 284 26918-26927 (2009)
  9. Interaction between the SH3 domain of Src family kinases and the proline-rich motif of HTLV-1 p13: a novel mechanism underlying delivery of Src family kinases to mitochondria. Tibaldi E, Venerando A, Zonta F, Bidoia C, Magrin E, Marin O, Toninello A, Bordin L, Martini V, Pagano MA, Brunati AM. Biochem. J. 439 505-516 (2011)
  10. NMR determines transient structure and dynamics in the disordered C-terminal domain of WASp interacting protein. Haba NY, Gross R, Novacek J, Shaked H, Zidek L, Barda-Saad M, Chill JH. Biophys. J. 105 481-493 (2013)
  11. A proline to glycine mutation in the Lck SH3-domain affects conformational sampling and increases ligand binding affinity. Bauer F, Sticht H. FEBS Lett. 581 1555-1560 (2007)
  12. Rhodium(II) metallopeptide catalyst design enables fine control in selective functionalization of natural SH3 domains. Vohidov F, Coughlin JM, Ball ZT. Angew. Chem. Int. Ed. Engl. 54 4587-4591 (2015)
  13. Roles for SH2 and SH3 domains in Lyn kinase association with activated FcepsilonRI in RBL mast cells revealed by patterned surface analysis. Hammond S, Wagenknecht-Wiesner A, Veatch SL, Holowka D, Baird B. J. Struct. Biol. 168 161-167 (2009)
  14. Altered dynamics in Lck SH3 upon binding to the LBD1 domain of Herpesvirus saimiri Tip. Weis DD, Kjellen P, Sefton BM, Engen JR. Protein Sci. 15 2402-2410 (2006)
  15. A Conserved residue in the yeast Bem1p SH3 domain maintains the high level of binding specificity required for function. Gorelik M, Stanger K, Davidson AR. J. Biol. Chem. 286 19470-19477 (2011)
  16. Distinct peptide binding specificities of Src homology 3 (SH3) protein domains can be determined by modulation of local energetics across the binding interface. Gorelik M, Davidson AR. J. Biol. Chem. 287 9168-9177 (2012)
  17. Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Galea CA, Mobli M, McNeil KA, Mulhern TD, Wallace JC, King GF, Forbes BE, Norton RS. Biochimie 94 608-616 (2012)
  18. The Binding of Syndapin SH3 Domain to Dynamin Proline-rich Domain Involves Short and Long Distance Elements. Luo L, Xue J, Kwan A, Gamsjaeger R, Wielens J, von Kleist L, Cubeddu L, Guo Z, Stow JL, Parker MW, Mackay JP, Robinson PJ. J. Biol. Chem. 291 9411-9424 (2016)
  19. High-resolution crystal structure of spectrin SH3 domain fused with a proline-rich peptide. Gushchina LV, Gabdulkhakov AG, Nikonov SV, Filimonov VV. J. Biomol. Struct. Dyn. 29 485-495 (2011)
  20. NMR studies of weak protein-protein interactions. Lian LY. Prog Nucl Magn Reson Spectrosc 71 59-72 (2013)
  21. The proline-rich region of 18.5 kDa myelin basic protein binds to the SH3-domain of Fyn tyrosine kinase with the aid of an upstream segment to form a dynamic complex in vitro. De Avila M, Vassall KA, Smith GS, Bamm VV, Harauz G. Biosci. Rep. 34 e00157 (2014)
  22. Hepatitis C virus NS5A is able to competitively displace c-Myc from the Bin1 SH3 domain in vitro. Aladag A, Hoffmann S, Stoldt M, Bösing C, Willbold D, Schwarten M. J. Pept. Sci. 20 334-340 (2014)
  23. Structural basis for recognition of the third SH3 domain of full-length R85 (R85FL)/ponsin by ataxin-7. Jiang YJ, Zhou CJ, Zhou ZR, Wu M, Hu HY. FEBS Lett. 587 2905-2911 (2013)
  24. A New Physiological Role for the DNA Molecule as a Protector against Drying Stress in Desiccation-Tolerant Microorganisms. García-Fontana C, Narváez-Reinaldo JJ, Castillo F, González-López J, Luque I, Manzanera M. Front Microbiol 7 2066 (2016)
  25. Most yeast SH3 domains bind peptide targets with high intrinsic specificity. Brown T, Brown N, Stollar EJ. PLoS ONE 13 e0193128 (2018)
  26. ASPP proteins discriminate between PP1 catalytic subunits through their SH3 domain and the PP1 C-tail. Bertran MT, Mouilleron S, Zhou Y, Bajaj R, Uliana F, Kumar GS, van Drogen A, Lee R, Banerjee JJ, Hauri S, O'Reilly N, Gstaiger M, Page R, Peti W, Tapon N. Nat Commun 10 771 (2019)
  27. Directed Evolution of a Highly Specific FN3 Monobody to the SH3 Domain of Human Lyn Tyrosine Kinase. Huang R, Fang P, Hao Z, Kay BK. PLoS ONE 11 e0145872 (2016)
  28. Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase. Berndt S, Gurevich VV, Iverson TM. PLoS ONE 14 e0215140 (2019)


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