Signal Transduction

The Interpro database (http://www.ebi.ac.uk/interpro/) integrates information from a range of so-called signature databases, including those mentioned above. Release 12.1 has 12953 protein entries and an inventory of 3585 domain types. However, the number of well characterized families is much smaller, of the order of 50–100.

Examples of domains with roles in signalling

A glance at the protein databases reveals the multidomain structure of many proteins, especially signalling proteins. As more domain types have been identified, it has become clear that the potential combinatorial diversity

is huge. As already discussed, signal propagation within cells commonly involves the formation of molecular complexes at particular cellular sites. Such complexes may contain catalytic domains that perform covalent modifications on substrate molecules that are then recognized by domains on other proteins (e.g. SH2 domains binding to phosphorylated tyrosine head groups).

Thus, in response to a ligand binding to its receptor and in a seemingly amorphous and disordered cytoplasm, organized signalling complexes are assembled which recruit yet other molecules to project the signal onwards. Interactions between domains lie at the heart of all this, but although we have accrued extensive information about their incidence in a wide range of proteins, our understanding of the mechanisms in which they take part is

limited. Importantly, for the reasons given above, the presence of a particular domain in a protein is no guarantee of function.

The list of domains in signalling proteins is large, and the electronic databases provide the most comprehensive source of information. Table 24.1 summarizes properties of domains that have received mention in previous chapters and the sections that follow provide illustrative examples of some of the most important.

Domains that bind oligopeptide motifs

SH2 domains

SH2 domains are exemplars of protein interaction domains that take part in signalling. They bind to short motifs containing a phosphotyrosine and were first observed in the viral non-receptor protein tyrosine kinase v-fps/fes, in the form of a regulatory region separate and distinct from the kinase domain. The region is conserved among other nrPTKs and is commonly located immediately N-terminal to the catalytic domain, (see Figure 17.1, page 514). It was named SH2 for Src homology region 2.6 In Src it regulates kinase activity through an intramolecular association with a phosphotyrosine near the

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Table 24.1  Examples of protein domains important in signalling

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Signal Transduction

Table 24.1  Continued

See end of chapter for abbreviations.

C-terminus. This keeps the kinase in a compact, inactive conformation. (The mechanism by which this inhibition is lifted is discussed below.) The affinity of SH2 domains for non-phosphorylated tyrosines or for phosphoserines or phosphothreonines is generally negligible.

SH2 domains are present in at least 110 different human proteins, which fall into 11 different functional classes.7 These may have catalytic activity, such as the receptor and non-receptor tyrosine kinases, RasGAP, phospholipase C , the regulatory subunits of PI3-kinase, and some protein tyrosine phosphatases. In all of these, the ability of the SH2 domain to bind to a phosphotyrosine has important consequences for enzyme activity. SH2 domain-containing proteins that are devoid of a catalytic activity, but carry other protein interaction domains, include adaptor proteins, typified by Grb2.

SH2 domains and protein tyrosine kinases are expressed throughout the animal kingdom, but they are less apparent in other eukaryotic organisms.

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Fig 24.1  SH2 domain of the Src kinase Lck.

The structure on the left shows the central -sheet and flanking helices. A rotated view is shown in the central panel. A polypeptide containing the -pYEEI- motif is depicted as spheres at the top of the figure. The bottom panel shows the polypeptide bound to the domain. The phosphotyrosine residue (salmon pink) makes a number of contacts with residues that line the pocket, including two arginines, one of which is displayed as grey and blue spheres. The isoleucine residue (yellow) is located in a hydrophobic cleft (1lcj.pdb10).

FIG 24.2  The PTB domain of IRS-1. Two views of the domain rotated 90° about a vertical axis. The right-hand

structure includes a phosphotyrosyl ligand (LVIAGNPApYRS, shown as blue sticks). Also indicated are three lysine residues (purple) that take part in binding to acidic phospholipid headgroups (1irs13).

structure is based on the highly conserved PH domain superfold

(see Figure 24.4) adopted by PH, EVH1, and a number of other protein interaction domains. The rigid -barrel, closed off at one end by a long -helix, provides a conserved scaffold, the surface of which has been adapted in different ways to bind diverse protein motifs or lipid head groups. Note that PH and EVH1 domains do not bind to phosphotyrosines and, despite their name, nor do a large number of PTB domains. The PTB domains that do, prefer

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