Domain architectural census of eukaryotic gene products containing O-protein phosphatases

Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases

Protein tyrosine phosphatases (PTPs) possess a conserved mobile catalytic loop, the WPD-loop, which brings an aspartic acid into the active site where it acts as an acid/base catalyst. Prior experimental and computational studies, focused on the human enzyme PTP1B and the PTP from Yersinia pestis, YopH, suggested that loop conformational dynamics are important in regulating both catalysis and evolvability. We have generated a chimeric protein in which the WPD-loop of YopH is transposed into PTP1B, and eight chimeras that systematically restored the loop sequence back to native PTP1B. Of these, four chimeras were soluble and were subjected to detailed biochemical and structural characterization, and a computational analysis of their WPD-loop dynamics. The chimeras maintain backbone structural integrity, with somewhat slower rates than either wild-type parent, and show differences in the pH dependency of catalysis, and changes in the effect of Mg2+. The chimeric proteins' WPD-loops differ significantly in their relative stability and rigidity. The time required for interconversion, coupled with electrostatic effects revealed by simulations, likely accounts for the activity differences between chimeras, and relative to the native enzymes. Our results further the understanding of connections between enzyme activity and the dynamics of catalytically important groups, particularly the effects of non-catalytic residues on key conformational equilibria.

Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes

The age of genomics has given us a wealth of information and the tools to study whole genomes. This, in turn, has facilitated genome-wide studies among organisms that were relatively less studied in the pre-genomic era or are non-model organisms. This paves the way to the discovery of interesting evolutionary patterns, which are brought to light by genome-wide surveys of protein superfamilies. Phosphorylation is a post-translational modification that is utilised across all clades of life, and acts as an important signalling switch, regulating several cellular processes. Tyrosine phosphatases, which are found predominantly in eukaryotes, act on phosphorylated tyrosine residues and sometimes on other substrates. Extending on our previous effort to look for tyrosine phosphatases in the human genome, we have looked for sequences of the cysteine-based tyrosine phosphatase superfamily in thirty mammalian genomes from all across Mammalia and validated the sequences with the presence of the signature catalytic motif. Domain architecture annotation, followed by in-depth analysis, revealed interesting taxon-specific patterns such as subtle differences between the protein families in marsupials and early mammals versus placental mammals. Finally, we discuss an interesting case of loss of the tyrosine phosphatase domain from a gene product in the course of eutherian evolution.

Genome-Wide Search for Tyrosine Phosphatases in the Human Genome Through Computational Approaches Leads to the Discovery of Few New Domain Architectures

Reversible phosphorylation maintained by protein kinases and phosphatases is an integral part of intracellular signalling, and phosphorylation on tyrosine is extensively utilised in higher eukaryotes. Tyrosine phosphatases are enzymes that not only scavenge phosphotyrosine but are also involved in wide range of signalling pathways. As a result, mutations in these enzymes have been implicated in the pathogenesis of several diseases like cancer, autoimmune disorders, and muscle-related diseases. The genes that harbour phosphatase domain also display diversity in co-existing domains suggesting the recruitment of the catalytic machinery in diverse pathways. We have examined the current draft of the human genome, using a combination of 3 sequence search methods and validations, and identified 101 genes encoding tyrosine phosphatase-containing gene products, agreeing with previous reports. Such gene products adopt 37 unique domain architectures (DAs), including few new ones and harbouring few co-existing domains that have not been reported before. This semi-automated computational approach for detection of gene products belonging to a particular superfamily can now be easily applied at whole genome level on other mammalian genomes and for other protein domains as well.