Can we infer peptide recognition specificity mediated by SH3 domains?

Cesareni, Gianni; Panni, Simona; Nardelli, Giuliano; Castagnoli, Luisa

doi:10.1016/s0014-5793(01)03307-5

Cited by 128 publications

(123 citation statements)

References 31 publications

(37 reference statements)

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“…Primary sequence analysis ( Figure 6A) indicated that the region of Tim between residues 23 and 57 contains a polyproline sequence that fits the consensus for type 1A ligands of SH3 domains, namely PXФXXPXXP, where P represents proline, X represents any amino acid, and Ф represents a hydrophobic amino acid (29). To test if the integrity of this region is important for maintenance of Tim autoinhibition, prolines within this sequence were individually mutated to alanine within the context of both full-length Tim and Tim (Δ22), and the mutated proteins were tested for an elevated capacity to activate RhoA in vitro.…”

Section: Tim Is Autoinhibited By a Proline-containing Region In Its Nmentioning

confidence: 99%

Role of the C-Terminal SH3 Domain and N-Terminal Tyrosine Phosphorylation in Regulation of Tim and Related Dbl-Family Proteins

2008

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Dbl-related oncoproteins are guanine nucleotide exchange factors (GEFs) specific for Rho-family GTPases and typically possess tandem Dbl (DH) and pleckstrin homology (PH) domains that act in concert to catalyze exchange. Although the exchange potential of many Dbl-family proteins is constitutively activated by truncation, the precise mechanisms of regulation for many Dbl-family proteins are unknown. Tim and Vav are distantly related Dbl-family proteins that are similarly regulated; their Dbl homology (DH) domains interact with N-terminal helices to exclude and prevent activation of Rho GTPases. Phosphorylation, substitution, or deletion of the blocking helices relieves this autoinhibition. Here we show that two other Dbl-family proteins, Ngef and Wgef, which like Tim contain a C-terminal SH3 domain, are also activated by tyrosine phosphorylation of a blocking helix. Consequently, basal autoinhibition of DH domains by direct steric exclusion using short Nterminal helices likely represents a conserved mechanism of regulation for the large family of Dblrelated proteins. N-Terminal truncation or phosphorylation of many other Dbl-family GEFs leads to their activation; similar autoinhibition mechanisms could explain some of these events. In addition, we show that the C-terminal SH3 domain binding to a polyproline region N-terminal to the DH domain of the Tim subgroup of Dbl-family proteins provides a unique mechanism of regulated autoinhibition of exchange activity that is functionally linked to the interactions between the autoinhibitory helix and the DH domain.The activation cycle of Rho GTPases 1 is tightly controlled by three families of proteins: GTPase-activating proteins (GAPs), guanine nucleotide dissociation inhibitors (GDIs), and guanine nucleotide exchange factors (GEFs). The Dbl family of proteins constitutes the largest group of GEFs specific for Rho GTPases. Dbl-family proteins are characterized by a Dbl homology (DH) domain, which contacts the Rho GTPase to catalyze nucleotide exchange by promoting and stabilizing an intermediate, nucleotide-free GTPase state, and an associated pleckstrin homology (PH) domain, which fine-tunes the exchange process. The 69 human Dbl-

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Section: Tim Is Autoinhibited By a Proline-containing Region In Its Nmentioning

confidence: 99%

Role of the C-Terminal SH3 Domain and N-Terminal Tyrosine Phosphorylation in Regulation of Tim and Related Dbl-Family Proteins

2008

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“…Typically, they bind to ligands with a proline-rich segment harboring the consensus sequence PXXP. The ligand adopts a helical polyproline type II conformation and interacts with the SH3 domain in either one of two opposite orientations (33). Accordingly, the ligands have been grouped in class I (consensus motif ϩXXPXXP, where ϩ denotes a positively charged amino acid) or class II (consensus motif PXXPXϩ).…”

Section: Fig 4 Interaction Of Zyxin With Lasp-1 As Demonstrated By mentioning

confidence: 99%

Zyxin Interacts with the SH3 Domains of the Cytoskeletal Proteins LIM-nebulette and Lasp-1

Zhuang

Trüeb

2004

Journal of Biological Chemistry

142

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Focal adhesions are essential cellular structures of metazoan organisms that link the extracellular matrix to the cytoskeleton. The controlled assembly and disassembly of focal adhesions is critical for a diversity of biological functions, including cell adhesion, motility, and spreading. Typically, focal adhesions are found at sites where a number of proteins from different signaling pathways converge to respond to extracellular signals (1). Thus far, more than 50 different focal adhesion proteins have been identified (2). Among them are several adapter proteins with protein-protein interaction motifs that play an important role in the dynamic assembly of focal adhesions.One of these adapter proteins is zyxin. Zyxin was originally identified in chicken fibroblasts as a protein associated with stress fibers and focal adhesions (3). The mammalian homologue of avian zyxin was subsequently cloned from a subtracted cDNA library enriched with clones that are down-regulated in transformed fibroblasts (4). At the same time, human zyxin was also cloned from umbilical vein endothelial cells by crosshybridization (5). Analysis of the protein sequence revealed the typical structure of a multidomain protein. At the C terminus, zyxin contains three LIM domains arranged in tandem. LIM domains are cysteine-rich motifs with two zinc finger-like structures that mediate specific protein-protein interactions. Three different binding partners for the LIM domains of zyxin have been identified, namely, the cysteine-rich protein CRP, the adapter protein p130cas, and the tumor suppressor protein H-warts/LATS1 (6 -8). At the N terminus, zyxin features an extended, proline-rich domain, which contains a nuclear export signal and several proline clusters. By virtue of these proline clusters, zyxin binds to proteins of the Ena/VASP family, which control the assembly and disassembly of actin filaments (9). The proline clusters also serve as docking sites for the oncoprotein Vav, a nucleotide exchange factor for the Rho family of GTPases (10). Moreover, the extended N-terminal domain is responsible for the interaction of zyxin with the actin-bundling protein ␣-actinin (11). We have recently demonstrated that a linear sequence motif found at the extreme N terminus of zyxin is essential for this interaction (12, 13). Our observation is supported by the fact that LPP (lipoma preferred partner), another member of the zyxin family containing the same linear motif, binds to ␣-actinin, too (14).Several pieces of evidence from different lines of investigation suggest that zyxin might play an important role in the organization of the actin cytoskeleton. Zyxin induces the polymerization of actin on the surface of mitochondria when artificially targeted to these ectopic sites (15,16). Actin polymerization and the resulting tension appear to be crucial for the dynamic assembly of focal adhesions (1). On the other hand, zyxin is one of the first molecules that dissociate from dissolving focal adhesions (17). This observation raises the intriguing possibil...

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“…Such interactions are unlikely to reveal themselves by gazing at mutagenized ligand sequences, in the absence of high resolution structural data for the ligand-SH3 complexes. It is worth noting that such overlapping motifs are not unique to the titin family and have been alluded to occasionally in several SH3-binding proteins with proline-rich motifs (52).…”

Section: Discussionmentioning

confidence: 99%

Titin as a Giant Scaffold for Integrating Stress and Src Homology Domain 3-mediated Signaling Pathways

Ma¹,

Forbes²,

Gutierrez-Cruz

et al. 2006

Journal of Biological Chemistry

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The richness of proline sequences in titins qualifies these giant proteins as the largest source of intrinsically disordered structures in nature. An extensive search and analysis for Src homology domain 3 (SH3) ligand motifs revealed a myriad of broadly distributed SH3 ligand motifs, with the highest density in the PEVK segments of human titin. Besides the canonical class I and II motifs with opposite orientations, novel overlapping motifs consisting of one or more of each canonical motif are abundant. Experimentally, the binding affinity and critical residues of these putative titinbased SH3 ligands toward nebulin SH3 and other SH3-containing proteins in muscle and non-muscle cell extracts were validated with peptide array technology and by the sarcomere distribution of SH3-containing proteins. A 28-mer overlapping motif-containing PEVK module binds to nebulin SH3 in and around the canonical cleft, especially to the acidic residues in the loops, as revealed by NMR titration. Molecular dynamics and molecular docking studies indicated that the overlapping motif can bind in opposite orientations with comparable energy and contact areas and predicts correctly orientation-specific contacts in NMR data. We propose that the overlap ligand motifs are a new class of ligands with innate ability to dictate SH3 domain orientation and to facilitate the rate, strength, and stereospecificity of receptor interactions. Prolinerich sequences of titins are candidates as major hubs of SH3-dependent signaling pathways. The interplay of elasticity and dense clustering of mixed receptor orientations in titin PEVK segment have important implications for the mechanical sensing, force sensitivity, and inter-adapter interactions in signaling pathways.

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Can we infer peptide recognition specificity mediated by SH3 domains?

Cited by 128 publications

References 31 publications

Role of the C-Terminal SH3 Domain and N-Terminal Tyrosine Phosphorylation in Regulation of Tim and Related Dbl-Family Proteins

Role of the C-Terminal SH3 Domain and N-Terminal Tyrosine Phosphorylation in Regulation of Tim and Related Dbl-Family Proteins

Zyxin Interacts with the SH3 Domains of the Cytoskeletal Proteins LIM-nebulette and Lasp-1

Titin as a Giant Scaffold for Integrating Stress and Src Homology Domain 3-mediated Signaling Pathways

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