- Topics in Current Genetics
- Protein Phosphatases (Topics in Current Genetics) by Joaquín Arino,Denis Alexander PDF
- e-book Protein Phosphatases (Topics in Current Genetics)
Topics in Current Genetics
We have surveyed the genome, for PPs using sensitive sequence analysis methods as described below: Domain assignments have been made for PP catalytic domain containing gene products using: 1 HMMer by querying each of the phosphatase domain containing proteins against all the protein family HMMs available in the Pfam database release Pfam InterPro, provides a powerful tool for protein sequence classification and function prediction.
It has been used in many genome annotation projects, as well as by UniProt curators for individual protein sequence annotation . InterPro picked all the sequences predicted by Pfam as it integrates Pfam in its search. CELLO v. Multiple alignments were constructed using ClustalW . Evolutionary relationships were studied using phylogenetic analysis package Mega4. Protein phosphatases, like many other signaling molecules, can be inhibited or activated by small molecules that occur naturally in the cell . Total number of functional PPs encoded in the genomes of some of the protozoan parasites  —  is shown in Figure 1.
The genome of E. It was observed that E. The percentage of protein phosphatases genes in the proteome complement is provided against every bar. To confirm the presence of phosphatase family domain the PPs retrieved through InterPro were searched for structural phosphatase domains. The E. The numbers of PPs obtained at different steps of the analysis are shown in Figure 2.
The distribution of PPs into various families is summarized in Table 1 along with subfamily assignments and other domains that are tethered to phosphatase catalytic domains. PPs are classified based on characteristics such as sequence, structure and phosphoamino-acid specificity. We predicted a total of STPs in E. Out of putative STPs in E. In contrast to PPP, members of the PPM family do not have regulatory subunits but contain instead additional domains and conserved sequence motifs that may help determine substrate specificity.
The HAD family, includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates  , .
Kutuzov et. PTPs are the key regulatory components in signal transduction pathways, cell cycle control and are important in the control of cell growth, proliferation, differentiation and transformation. Among the 79 PTPs identified in E.
Protein Phosphatases (Topics in Current Genetics) by Joaquín Arino,Denis Alexander PDF
Classical PTPs are strictly tyr-specific sharing a common cysteine-based mechanism of catalysis  , . These enzymes have low sequence similarity beyond the cysteine-containing motif and smaller catalytic domains than the classical PTPs. Their catalytic machinery is very similar to that of class I enzymes, they are structurally unrelated . LMPTPs are highly conserved throughout evolution from yeasts to man and highly homologous genes are even seen in prokaryotes.
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The protein histidine phosphatases PHP is a large functionally diverse group of proteins. In contrast to cysteine-dependent PTPs, PHPs utilize histidine, rather than cysteine, for substrate dephosphorylation . EEP family is a structural domain found in the large family of proteins. EEPs include magnesium dependent endonucleases and many phosphatases involved in intracellular signalling  , .
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This large superfamily includes a diverse set of proteins Table 1. Inositol phosphatases belong to different families of enzymes; PTEN phosphotase and tensin homolog and myotubularin inositol 3-phosphatases belong to PTP superfamily. In parasites, a proper ion balance is essential for them to be able to invade and live in other organisms. Membrane-bound pyrophosphatases cannot be found in humans but they are crucial for the survival of protozoan parasites.
Membrane proteins in general are important targets for drugs . Inorganic pyrophosphate has been shown to be necessary for the growth of Escherichia coli and for yeast mitochondrial function  , . Understanding the structure and function of pyrophosphatases will help us in designing specific drugs to disturb its function.
The presence of varying numbers of leucine-rich repeat LRR domain is an unusual feature of some of the phosphatases, which may be involved in protein—protein interactions.
The LRRs may be associated in interaction with host cell and pathogenesis of the parasite. Unexpectedly, LRRs have been shown to be associated with microbial virulence factors helping in the interaction with host cells and infection establishment . We have observed several proteins with non-functional phosphatase domain, these proteins were named as pseudophosphatases. Several members of the PTP superfamily possess conserved domains with core features of a PTP, but which lack residues that are critical for catalysis .
Pseudophosphatases are most prevalent among the Myotubularins sub-family from PTP superfamily. Three such proteins were predicted in E. Recently, it has been demonstrated that inactive myotubularins form complexes with the active enzymes. These interactions regulate both the enzymatic activity and the subcellular location of the active phosphatase .
It appears that the presence of such PPs may have an important role in virulence. There are several hypothetical proteins, which are not studied at all so far but we have identified phosphatase domains in these proteins and we named it as unidentified PPs. Our analysis has added to the list of PPs whose functions are not yet well understood.
We have identified at least 39 gene products with a clear similarity to PPs, but to the best of our knowledge these genes are unexplored by experimental analysis. A list of these phosphatases with their domain assignments is shown in Table S4 in file SI. The catalytic domains in most of these hypothetical proteins could be associated to known families of PPs because of a high similarity of the catalytic regions. Based on the amino acid sequence, two hundred fifty E. From the phylogenetic analysis of STP family it was observed that it consists of two branches with one branch consisting strictly of PPPs except for one PPM family member.planaldegechest.tk
e-book Protein Phosphatases (Topics in Current Genetics)
The other branch composed of sub-branches from all the three families of STP family Figure 4. Pyrophosphatases form two distantly related families consisting of one branch only of dUTPases and other inorganic phosphatases Figure 7. The phylogenetic classification also confirms that hypothetical proteins are showing close relationship to the members of the assigned families. Branches with diamond shapes represents hypothetical proteins. Branches with diamond shapes represent hypothetical proteins. The dephosphorylation of proteins is catalyzed by PPs, acting antagonistically to PKs.
PPs are apparently less attractive drug targets, because they typically act on a broader range of proteins than kinases do. In many parasitic diseases, a gain of specific phosphatase function may contribute to the pathology. In parasites like E. In such instances, these phosphatases may serve as appropriate drug targets.
A comphrensive analysis shows that E. A large number of PPs manifests protein phosphorylation as the key mechanism of signal transduction in the parasite. Several members were seen from the new family of phosphatases INPP5 family that do not have homologs in humans. Proteins from the pyrophosphatase family which are crucial for the survival of the parasite were also identified. This indicates that members of the INPP5 and pyrophosphatase family can act as good drug targets. Several phosphatases in combination with LRRs were also seen, the involvement of LRRs in microbial pathogenesis and their capability to bind to a vast array of structurally unrelated ligands make them a potential target for vaccines and new drugs.
Few pseudophosphatases were also identified, these are suggested to be involved in virulence of the parasite . In particular, protein phosphorylation is a major currency of signal transduction pathways. Exploring the conditions under which the cells employ two different kinetic mechanisms for dephosphorylation will help us to understand more about the evolutionary adaptation of organisms.