Ssu72 Results

Function

BLAST results

Running a protein BLAST search on 'serine phosphatase of RNA polymerase II CTD (SSU72 superfamily)' from Drosophila melenogaster (the 'Drosophila Ssu72 protein') returned a large number of highly relevant (bit score > 200) sequences that were of a very similar length (see Figure 1) to that of the query. However, the first 27 of those sequences were not considered relevant for the purposes of this paper for a number of reasons. For instance, some were merely homologous proteins in other closely related Drosophila species that had been identified in a similarly automated manner to this one and for which there were no PubMed publications available and thus no information that could be used to easily infer functionally relevant details. Similarly, other proteins, in more distantly related organisms, had not been functionally characterised by experimentation or structural analysis, because they had been identified by high-throughput sequencing and had seen minimal, if any, human input. Some BLAST hits were labelled as hypothetical proteins and were therefore not necessarily protein coding and biologically expressed. Notwithstanding this, the first relevant protein identified was 'SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)', the human Ssu72 protein, for which there were a small number of articles available on PubMed (see Figure 2), as well as expression data from SymAtlas (see Figure 3). This protein was also found to have a 60.21% sequence identity with the Drosophila Ssu72 protein, with no gaps in the alignment. Thus, a review of the literature surrounding it was considered a suitable entry-point in the process of this analysis.

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  Figure 1: BLAST result for the Drosophila Ssu72 protein. Hits highlighted in grey were not considered in this analysis. The human Ssu72 protein is indicated by the black bar.

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  Figure 2: PubMed results for human Ssu72 protein.

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  Figure 3: Expression profile for the human Ssu72 protein.

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  Figure 4: Multiple sequence alignment of Drosophila Ssu72 (query) and Human Ssu72 (sbjct) from BLAST result.

Literature review and ProFunc result

The human Ssu72 protein, for which there exist a number of mammalian homologues, was first proposed to function as a protein tyrosine phosphatase (Meinhart, Silberzahn, & Cramer, 2003). Therefore, a ProFunc analysis was carried out on our candidate protein, Drosophila Ssu72, with the purpose of comparing components of its primary and secondary structure with proteins that do not necessarily have a high level of overall sequence similarity and thus would be unlikely to surface on a non-targeted search of a large database (ie.by BLAST). Despite offering a number of powerful results (see Figures 4 - 8), the ProFunc analysis of the Drosophila Ssu72 protein returned just two sets of informative data. The first of these was from the SSM (Secondary Structure Matching) program, which 'identifies proteins in the PDB that have a similar fold to that of the query structure' (Krissinel & Henrick, 2004).

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  Figure 4: First section of ProFunc result summary.

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  Figure 5: Second section of ProFunc results.

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  Figure 6: Third section of ProFunc results.

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  Figure 7: Fourth section of ProFunc results.

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  Figure 8: Fifth section of ProFunc results.

Krissinel E and Henrick K (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Cryst., D60, 2256-2268.

Structure

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Abstract | Introduction | Results | Discussion | Conclusion | Method | References