Polyproline binding domains

Upon binding, the artificial transcription factor recruits the necessary transcriptional machinery for gene activation. (Bottom, left) Ball-and-stick model for a polyamide conjugated to the VP2 activation domain. Symbols are as in Fig. 3.4. (Bottom, right) Structure of the polyamide-VP2 conjugate with the polyproline linker domain in brackets... 

The crystal structure of the peptide substrate-binding domain (140—245 of 517 residues of human al subunit) of the human type I enzyme forms 2.5 tetratricopeptide (TPR) repeat domains with five a helices (PDB accession number ITJC). The organization of tyrosine residues is suggested to be key to its interaction with the substrate peptide in a polyproline II helix. The TPR motif is composed of a 34 amino acid repeated a helical motif, and is typically involved in protein-protein interactions. The tandem repeats of TPR motifs are found in many proteins related to chaperone, cell cycle, transcription, and protein transport... 

Figure 13.30 Ribbon diagram of the structure of Src tyrosine kinase. The structure is divided in three units starting from the N-terminus an SH3 domain (green), an SH2 domain (blue), and a tyrosine kinase (orange) that is divided into two domains and has the same fold as the cyclin dependent kinase described in Chapter 6 (see Figure 6.16a). The linker region (red) between SH2 and the kinase is bound to SH3 in a polyproline helical conformation. A tyrosine residue in the carboxy tail of the kinase is phosphorylated and bound to SH2 in its phosphotyrosine-binding site. A disordered part of the activation segment in the kinase is dashed. (Adapted from W. Xu et al.. Nature 385 595-602, 1997.)...

Src tyrosine kinase contains both an SH2 and an SH3 domain linked to a tyrosine kinase unit with a structure similar to other protein kinases. The phosphorylated form of the kinase is inactivated by binding of a phosphoty-rosine in the C-terminal tail to its own SH2 domain. In addition the linker region between the SH2 domain and the kinase is bound in a polyproline II conformation to the SH3 domain. These interactions lock regions of the active site into a nonproductive conformation. Dephosphorylation or mutation of the C-terminal tyrosine abolishes this autoinactivation. 

WW domains (named after the one letter abbreviation for the amino acid tryptophan) are small regions of around 30 residues, which, like SH3 domains, bind to polyproline sequences. These sequences often contain the consensus sequence PPXY or PPLP. Examples of proteins that contain WW domains include Nedd4 E3 ubiquitin ligase (Fig. 1) and IQGAP1. 

Protein-protein interaction domain that binds to polyproline motifs with the sequence PXXP. Particularly important in assembling protein complexes at activated receptors which contain intrinsic tyrosine kinases. 

Protein-protein interaction domain which, like SH3 domains, bind to polyproline sequences. 

Molecular insight into the protein conformation states of Src kinase has been revealed in a series of x-ray crystal structures of the Src SH3-SH2-kinase domain that depict Src in its inactive conformation [7]. This form maintains a closed structure, in which the tyrosine-phosphorylated (Tyr527) C-terminal tail is bound to the SH2 domain (Fig. 2). The x-ray data also reveal binding of the SH3 domain to the SH2-kinase linker [adopts a polyproline type II (PP II) helical conformation], providing additional intramolecular interactions to stabilize the inactive conformation. Collectively, these interactions cause structural changes within the catalytic domain of the protein to compromise access of substrates to the catalytic site and its associated activity. Significantly, these x-ray structures provided the first direct evidence that the SH2 domain plays a key role in the self-regulation of Src. 

The binding of interaction domains to their targets is not always dependent on post-translational modifications. Notably, a number of modules, including SH3, WW and EVHl domains, recognize short proline-rich motifs that adopt a polyproline type II helix, and these interactions... 

The p,-ARs contain polyproline motifs within their intracellular domains, which in other proteins are known to mediate interactions with SH3 domains. Using the proline-rich third intracellular loop of the (3 r AR as bait, T ang et al. (41) identified SH3p4/p8/pl3 (also referred to as endophilin 1/2/3), a SH3 domain-containing protein family, as binding partners for (3rARs. Both in vitro and in... 

Functional domains are substantially larger parts of proteins. For example, an SH2 domain is a sequence of around 100 amino acids (Fig. 3.8) that forms a functional unit that binds specifically tophosphotyrosine similarly, an SH3 domain forms a functional unit that binds to polyproline sequence motifs. Functional domains have been identified... 

Other negative correlations are simpler to interpret. Two functionally antagonistic enzymes, namely, protein kinases and protein phosphatases, have, to date, not been found in the same protein. Similarly, WW and SH3 domains that both bind the similar polyproline-containing substrates are never found together. This last finding, however, is curious since 216 proteins that contain either two or more WW, or two or more SH3, domains are known. Finally, it appears that proteins with domains that bind phosphoserine or phosphothreonine (FHA, fork-head-associated domains) never contain domains that bind phosphoty-rosine (SH2, PTB, and PTBI domains). This indicates that cytoplasmic signaling via phosphoserine or phosphothreonine occurs via pathways distinct from those signaling via phosphotyrosine. 

V. Uryga-Polowy, D. KossUck, C. Freund, J. Rademann, Resin-bound aminofluorescein for C-terminal labeling of peptides high-affinity polarization probes binding to polyproline-specific GYF domains. Chembiochem 2008, 9, 2452 2462. 

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