Phosphorylation of unique domains of Src family of kinases

Members of the Src family of kinases (SFKs) are non-receptor tyrosine kinases involved in numerous signal transduction pathways. The catalytic, SH3 and SH2 domains are attached to the membrane-anchoring SH4 domain through the intrinsically disordered"Unique" domains, which exhibit strong sequence divergence among SFK members. In the last decade, structural and biochemical studies have begun to uncover the crucial role of the Unique domain in the regulation of SFK activity. This mini-review discusses what is known about the phosphorylation events taking place on the SFK Unique domains, and their biological relevance. The modulation by phosphorylation of biologically relevant inter- and intra- molecular interactions of Src, as well as the existence of complex phosphorylation/dephosphorylation patterns observed for the Unique domain of Src, reinforces the important functional role of the Unique domain in the regulation mechanisms of the Src kinases and, in a wider context, of intrinsically disordered regions in cellular processes

The SH3 domain acts as a scaffold for the N-terminal intrinsically disordered regions of c-Src

Regulation of c-Src activity by the intrinsically disordered Unique domain has been recently demonstrated. However, its connection with the classical regulatory mechanisms is still missing. Here we show that the Unique domain is part of a long loop closed by the interaction of the SH4 and SH3 domains. The conformational freedom of the Unique domain is further restricted through direct contacts with SH3 that are allosterically modulated by binding of a poly-proline ligand in the presence and in the absence of lipids. Our results highlight the scaffolding role of the SH3 domain for the c-Src N-terminal intrinsically disordered regions and suggest a connection between the regulatory mechanisms involving the SH3 and Unique domains

Multi-phosphorylation of the intrinsically disordered unique domain of c-Src studied by in-cell and real-time NMR

Intrinsically disordered regions (IDRs) are preferred sites for post-translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase-phosphatase networks. Here we used real-time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the 'unique domain' of c-Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin-dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP-dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK-dependent sites, thus suggesting indirect effects of kinase-phosphatase networks. This study provides a proof-of-concept of the use of real-time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains

Evidence for conserved fuzzy complexes involving a preorganized Unique domain in the Src family of kinases

The N-terminal regulatory region of c-Src including the SH4, Unique and SH3 domains adopts a compact, yet highly dynamic, structure that can be described as an intramolecular fuzzy complex. Most of the long-range interactions within the Unique domain are also observed in constructs lacking the structured SH3, indicating a considerable degree of preorganization of the disordered Unique domain. Here we report that members of the Src family of kinases (SFK) share well-conserved sequence features involving aromatic residues in their Unique domains. This observation contrasts with the supposed lack of sequence homology implied by the name of these domains and suggests that the other members of SFK also have a regulatory region involving their Unique domains. We argue that the Unique domain of each SFK is sensitive to specific input signals, encoded by each specific sequence, but the entire family shares a common mechanism for connecting the disordered and structured domains

Structural and functional characterization of the intrinsically disordered Unique domain of c-Src

[cat] Aquesta tesi, titulada “Caracterització estructural i funcional del domini únic intrínsecament desplegat de c-Src humana”, aborda els aspectes fonamentals de la funció biològica del domini Únic intrínsecament desordenat de c-Src (USrc) que fins ara ha sigut poc estudiat. Hem caracteritzat primer mitjançant tècniques de biologia estructural als efectes de les mutacions de la ULBR (Unique Lipid Binding Region) dirigides al lloc de les interaccions descrites anteriorment amb els lípids i amb el domini SH3. Llavors, hem investigat els esdeveniments de fosforilació que tenen lloc en el domini únic per tècniques de RMN en cèl•lules. Finalment, hem demostrat el paper funcional de USRC en el context de línies de cèl•lules normals i canceroses. En conjunt, els nostres resultats han demostrat que el domini únic de c-Src participa activament en el mecanisme de regulació en què la tirosina quinasa c-Src està implicada. Aquest estudi representa una nova fita essencial en la comprensió de com c-Src pot controlar una àmplia varietat d'esdeveniments de senyalització dins de les cèl•lules. A més, té el potencial d'obrir el camí a la possibilitat de noves aplicacions per al tractament del càncer mitjançant el desenvolupament de nous fàrmacs selectius dirigits residus actius funcionals localització en el domini únic. Aquesta tesi constitueix una "prova de concepte" de com des de la comprensió atomista d'un tema d'interès (enfocament estructural) pot ser possible entendre i successivament demostrar la importància biològica dels fenòmens observats (enfocament funcional).[eng] Objectives: Objective 1 – Effect of mutations perturbing the ULBR of the Unique domain of c-Src. The first objective of this thesis was the in vitro characterization of the effect of mutations in the ULBR on the previously determined main interactions of the Unique domain: binding to lipids and to the SH3 domain. Objective 2 - Phosphorylation of c-Src Unique domain in Xenopus laevis oocytes and mammalian cell extracts. Phosphorylation of the Unique domain of c-Src is one of the modulation parameters affecting lipid binding and had previously been reported to affect c-Src activity. The second objective was to study the phosphorylation of the isolated Unique domain in Xenopus laevis oocytes, that enabled the study of phosphorylation in a living cell and in cell extracts, that allowed further manipulation of the phosphatase/kinase network. Objective 3 - Functional studies of the Unique domain in the context of the full-length protein. The last objective was the evaluation of the functional significance of the modifications investigated in the isolated Unique domain as objectives 1 and 2 in a human colorectal cell line and in the context of the full length protein. The present thesis addressed fundamental aspects of the biological role of the intrinsically disordered Unique domain of c-Src that until now was poorly understood. We have first characterized through a structural biology approach the effects of sitedirected ULBR mutations on the previously described interactions with lipids and with the folded SH3 domain. Then, we have investigated the phosphorylation events taking place on the Unique domain by state-of-the-art in-cell NMR techniques. Finally, we have shown the functional role of USrc in the context of normal and cancer cell lines. All together, our results have demonstrated that the Unique domain of human c-Src actively participates in the regulation mechanism in which the tyrosine kinase c-Src is involved. This study represents a new essential milestone in the understanding of how c-Src can control a wide variety of signaling events inside cells. Furthermore, it potentially opens the way to the possibility of new applications for cancer therapy through the development of novel selective drugs targeting functional active residues locating in the Unique domain. This thesis represents a “proof-of-concept” of how from the atomistic comprehension of a subject of interest (structural approach) it can be possible to understand and successively demonstrate the biological significance of the observed phenomena (functional approach). Conclusions: - Mutations in the Unique Lipid Binding Region affect the lipid binding capability of USrc but not the inter-domain interaction with the folded SH3. - Disruption of the conserved FGGF motif causes important local effects that affect the structure of the ULBR. - The SH3 domain of human c-Src loses its ability to interact with lipids in presence of a polyproline peptide. - Real-time NMR spectroscopy allowed the study of complex phosphorylation/dephosphorylation processes in USrc mediated by kinases and phosphatases in Xenopus laevis derived cells or cell extracts. - Three different phosphorylation sites present in the Unique domain that were unequivocally assigned to Ser 17, Ser 69 and Ser 75 have been identified in Xenopus laevis, COS-7, MEFs and HeLa cell systems. - It was the first time that phosphorylation of Ser 69 of c-Src was observed in those model systems. - The biological relevance of the ULBR has been firstly demonstrated in Xenopus laevis oocytes in the context of the full-length c-Src. - The functional roles of the described phosphorylation events together with ULBR mutations have been shown in HEK293T cells and in the human colorectal SW620 cancer cell lines in the context of the full-length protein. - A “positional regulation model” has been proposed as a new c-Src selectivity regulation mechanism

Phosphorylation of unique domains of Src family of kinases

Members of the Src family of kinases (SFKs) are non-receptor tyrosine kinases involved in numerous signal transduction pathways. The catalytic, SH3 and SH2 domains are attached to the membrane-anchoring SH4 domain through the intrinsically disordered"Unique" domains, which exhibit strong sequence divergence among SFK members. In the last decade, structural and biochemical studies have begun to uncover the crucial role of the Unique domain in the regulation of SFK activity. This mini-review discusses what is known about the phosphorylation events taking place on the SFK Unique domains, and their biological relevance. The modulation by phosphorylation of biologically relevant inter- and intra- molecular interactions of Src, as well as the existence of complex phosphorylation/dephosphorylation patterns observed for the Unique domain of Src, reinforces the important functional role of the Unique domain in the regulation mechanisms of the Src kinases and, in a wider context, of intrinsically disordered regions in cellular processes

The SH3 domain acts as a scaffold for the N-terminal intrinsically disordered regions of c-Src

Regulation of c-Src activity by the intrinsically disordered Unique domain has been recently demonstrated. However, its connection with the classical regulatory mechanisms is still missing. Here we show that the Unique domain is part of a long loop closed by the interaction of the SH4 and SH3 domains. The conformational freedom of the Unique domain is further restricted through direct contacts with SH3 that are allosterically modulated by binding of a poly-proline ligand in the presence and in the absence of lipids. Our results highlight the scaffolding role of the SH3 domain for the c-Src N-terminal intrinsically disordered regions and suggest a connection between the regulatory mechanisms involving the SH3 and Unique domains

Evidence for conserved fuzzy complexes involving a preorganized Unique domain in the Src family of kinases

The N-terminal regulatory region of c-Src including the SH4, Unique and SH3 domains adopts a compact, yet highly dynamic, structure that can be described as an intramolecular fuzzy complex. Most of the long-range interactions within the Unique domain are also observed in constructs lacking the structured SH3, indicating a considerable degree of preorganization of the disordered Unique domain. Here we report that members of the Src family of kinases (SFK) share well-conserved sequence features involving aromatic residues in their Unique domains. This observation contrasts with the supposed lack of sequence homology implied by the name of these domains and suggests that the other members of SFK also have a regulatory region involving their Unique domains. We argue that the Unique domain of each SFK is sensitive to specific input signals, encoded by each specific sequence, but the entire family shares a common mechanism for connecting the disordered and structured domains