Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Apr 4;2015:bav031.
doi: 10.1093/database/bav031. Print 2015.

dbPSP: A Curated Database for Protein Phosphorylation Sites in Prokaryotes

Affiliations
Free PMC article

dbPSP: A Curated Database for Protein Phosphorylation Sites in Prokaryotes

Zhicheng Pan et al. Database (Oxford). .
Free PMC article

Abstract

As one of the most important post-translational modifications, phosphorylation is highly involved in almost all of biological processes through temporally and spatially modifying substrate proteins. Recently, phosphorylation in prokaryotes attracted much attention for its critical roles in various cellular processes such as signal transduction. Thus, an integrative data resource of the prokaryotic phosphorylation will be useful for further analysis. In this study, we presented a curated database of phosphorylation sites in prokaryotes (dbPSP, Database URL: http://dbpsp.biocuckoo.org) for 96 prokaryotic organisms, which belong to 11 phyla in two domains including bacteria and archaea. From the scientific literature, we manually collected experimentally identified phosphorylation sites on seven types of residues, including serine, threonine, tyrosine, aspartic acid, histidine, cysteine and arginine. In total, the dbPSP database contains 7391 phosphorylation sites in 3750 prokaryotic proteins. With the dataset, the sequence preferences of the phosphorylation sites and functional annotations of the phosphoproteins were analyzed, while the results shows that there were obvious differences among the phosphorylation in bacteria, archaea and eukaryotes. All the phosphorylation sites were annotated with original references and other descriptions in the database, which could be easily accessed through user-friendly website interface including various search and browse options. Taken together, the dbPSP database provides a comprehensive data resource for further studies of protein phosphorylation in prokaryotes. Database URL: http://dbpsp.biocuckoo.org

Figures

Figure 1.
Figure 1.
The schema of the construction processes and contents for the dbPSP database.
Figure 2.
Figure 2.
The distributions of residues types and species for the phosphoproteins in prokaryotes. (A) The distributions of residues types. (B) The distribution of phyla.
Figure 3.
Figure 3.
The browse options of dbPSP database. (A) Browse option by residue types. (B) Browse option by phyla. (C) The tyrosine phosphorylated phosphoprotein list in. (D) The detailed information of phosphorylated serine hydroxymethyltransferase from E. coli (strain K12).
Figure 4.
Figure 4.
The search options of dbPSP database. (A) The database could be searched by simple key words. (B) The ‘Advanced Search’ allowed users to submit up to three terms for search. (C) The ‘Batch Search’ for retrieving multiple protein entries with a list of terms. (D) The database could be queried with a protein sequence to find identical or homologous phosphoproteins.
Figure 5.
Figure 5.
Analyses of sequence preferences of phosphorylation sites in prokaryotes. The sequence preferences of phosphorylation sites in bacteria (A), archaea (B) and eukaryotes (C) were presented with WebLogo. The comparisons of sequence preferences for bacteria and archaea (D), bacteria and eukaryotes (E), archaea and eukaryotes (F).
Figure 6.
Figure 6.
Statistical analyses of GO annotation for phosphoproteins in E. Coli k12 and S. acidocaldarius. (A) The enriched GO terms for phosphoproteins in E. Coli k12. (B) The enriched GO terms for phosphoproteins in S. acidocaldarius.

Similar articles

See all similar articles

Cited by 6 articles

See all "Cited by" articles

References

    1. Cohen P. (1982) The role of protein phosphorylation in neural and hormonal control of cellular activity. Nature, 296, 613–620. - PubMed
    1. Cohen P. (2002) The origins of protein phosphorylation. Nat. Cell Biol., 4, E127–E130. - PubMed
    1. Lipmann F.A., Levene P.A. (1932) Serinephosphoric acid obtained on hydrolysis of vitellinic acid. J. Biol. Chem., 98, 109–114.
    1. Tarrant M.K., Cole P.A. (2009) The chemical biology of protein phosphorylation. Annu. Rev. Biochem., 78, 797–825. - PMC - PubMed
    1. Ubersax J.A., Ferrell J.E., Jr (2007) Mechanisms of specificity in protein phosphorylation. Nat. Rev. Mol. Cell Biol., 8, 530–541. - PubMed

Publication types

Feedback