Ssu72 Discussion

Function

In attempting to infer the function of the Drosophila Ssu72 protein, two broad sources of information were used, each leading to distinct conclusions (the compatibility of which will be considered in due course). The value of the first data set as a proxy for experimental information about the functionally uncharacterised Drosophila protein is predicated on the high level of similarity in amino acid sequence and almost identical match in both secondary and 3D structure that was found to exist between this protein and the human Ssu72 protein. This data comprises both in vivo and in vitro functional analyses of the latter protein, which tend to suggest that the protein in Drosophila similarly functions as a serine phosphatase – presumably at the C-terminal domain of RNA polymerase II (Krishnamurthy et al., 2004) – and has a role in 3' end mRNA processing that is independent of its activity as a phosphatase. The second piece of guidance comes from the results generated by the use of computational and bioinformatic tools in this paper, which prima facie reveal the Drosophila protein to be a protein tyrosine phosphatase. Therefore, these two seemingly conflicting conclusions must now be evaluated on the basis of the limited evidence available to determine which is more likely to be true, or whether one necessarily precludes the other.

Protein Tyrosine Phosphatase?

An evaluation of the Drosophila protein as a potential Protein Tyrosine Phosphatase (PTPase) is a logical place to begin this discussion as this is what Meinhart, Silberzahn, & Cramer (2003) concluded about the human protein, based on their initial characterization of its primary, secondary and 3D structures, as well as a number of important pieces of experimental data. They began by identifying, within the amino acid sequence of the Ssu72 gene, the presence of a PTPase signature motiff at the N-terminal end. This motiff is a short sequence, the consensus sequence being (H/V)C(X)5R(S/T), which forms the phosphate-binding site (P-loop) in the mature protein and is where, invariably, members of the PTPase superfamily exert their catalytic action. This motiff is similarly present in the Drosophila Ssu72 protein and, what is more, shares almost the precise sequence as that of the human protein (VCSSNQNRS), but for an unknown amino acid in place of the glutamine (Q). Meinhart, Silberzahn, & Cramer (2003) inferred, based on this motiff, that if the human Ssu72 were a PTP, it would be one of the low molecular weight family. This inference was based on the presence of a characteristic asparagine (N) in the motiff, which the Drosophila protein shares. Further analysis of the amino acid sequence of the human protein found the presence of two important residues, which form part of an 'aspartate loop' that is important for the binding of substrate at the P-loop. Those residues are aspartates 140 and 143, both of which are present in the Drosophila protein and which were found, by mutational analysis, to contribute to the human protein's activity.

Meinhardt, Silberzahn, & Cramer (2003) went on to examine in vitro whether the human protein

In the structural results presented in this report, DaliLite was used to superimpose the 3D form of the Drosophila Ssu72 protein over inter alia a representative low molecular weight tyrosine phosphatase - Bovine Low Molecular Weight Ptpase (See figure 1).

According to Zhang (1998), 'amino acid sequence comparisons of the catalytic domains of PTPases with the catalytic subunits of protein Ser/Thr phosphatases have shown no sequence similarity'. This does necessarily mean that phosphatases with specificity for tyrosine cannot act on serine/threonine, but that if they do, it must be by a mechanism that has not been characterised thus far.

References

Zhang Z-Y. 1998 Protein-Tyrosine Phosphatases: Biological Function, Structural Characteristics, and Mechanism of Catalysis. Critical Reviews in Biochemistry and Molecular Biology, 33(1):1–52.

Structure

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Abstract | Introduction | Results | Discussion | Method | References