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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

¹ Lehrstuhl für Biopolymere, Universität Bayreuth, 95440 Bayreuth, Germany
² Institut für Biochemie, Emil-Fischer-Zentrum, Universität Erlangen–Nürnberg, 91054 Erlangen, Germany

(RECEIVED May 3, 2005; FINAL REVISION July 4, 2005; ACCEPTED July 5, 2005)

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.

Keywords: SH3 domain; Lyn; extended binding motif; ligand affinity; NMR; structure; complex; NMR spectroscopy; fluorescence; docking proteins

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051563605.

Reprint requests to: Heinrich Sticht, Institut für Biochemie, Emil-Fischer-Zentrum, Universität Erlangen–Nürnberg, Fahrstr. 17, 91054 Erlangen, Germany; e-mail: h.sticht{at}biochem.uni-erlangen.de; fax: +49-9131-8522485.

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