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Using PhosphoSite®

This section provides a description of how to use PhoshoSite v1.0, as well as an animated Site Map that provides a virtual tour of the site. Please note that we are constantly updating the web pages. In order to view the most recent versions of our pages it is important to frequently discard cache or temporary internet files.
The Homepage is the starting point for querying PhosphoSite. The user can chose from two sorts of queries.
° Simple Search allows the user to query the database to view all known phosphorylation sites in a specific protein. After you submit the name of a protein in the search interface, the Search Results page lists all proteins in PhosphoSite that contain the input name. If the desired protein is listed, the user can select that protein and will be taken to its corresponding Phosphoprotein Page (see below). View the PhosphoSitePlus® Training Tutorial.
° Advanced Search allows the user to simultaneously search from up to five categories of information, including protein name, the residue number of the phosphorylation site, SwissProt ID, author name, PubMed ID, CST Catalog#, domain, and sequence. For example, a user may look for a particular author's paper about a specific protein. Searching for a given domain will list all proteins that have a phosphorylation site within the domain of interest. Searching for a sequence, the user can find all occurrences of the sequence in proteins curated into PhosphoSite, either occurring in a phosphorylation site or elsewhere in the protein.

A Phosphoprotein Page summarizes information about the parent protein and the phosphorylation sites contained within it.
° The Overview section at the top of the page includes a brief description of the protein, protein type, the protein accession number used as the reference sequence by PhosphoSite, alternative names, and molecular weight. An interactive isoelectric calculator allows the user to retrieve the predicted isoelectric points of various phosphorylated isoforms of the parent protein. Links to other useful resources include the Alliance for Cellular Signaling (AfCS) (1), ScanSite (2), solved 3D structures from PDB, and the Protein Kinase Resource (PKR) (3).
° The Domains section in the middle of the page contains a linear schematic of the protein, predicted domains from Pfam (St. Louis) (4), and the location of known phosphorylation sites relative to the domain structure. Phosphosites that have curated records are underlined and hyperlinked to the Phosphorylation Site page (see below).
° The Sequences and Species section at the bottom page presents the phosphorylated residue and the surrounding amino acids (+/- 7) in the parent protein and orthologous sites in other species. Those residues that are underlined and hyperlinked are known to be phosphorlated in vivo : clicking on the link will take you to the Phosphorylation Site page (see below). A small icon next to the phosphosite indicates that phosphosite-specific antibodies or other probes are available for this site: clicking on the link will take you to either the CST catalog or to other sources of such reagents.

The Phosphorylation Site page serves information specific to the selected phosphosite. It contains three sections.
° The Phosphosite Information section at the top of the page includes the phosphorylated residue and its surrounding sequence (+/- 7 residues), a link to Scansite to predict likely sites for protein phosphorylation by particular kinases and likely sites for interaction with other signaling proteins (2), orthologous sites in other species, and a Blast search of the site against NCBI, SwissProt and PDB.
° The middle section contains information that has been curated about the phosphorylation site and may include information about how the site was experimentally characterized (mass spectrometry, phospho-antibodies, etc.), the apparent regulation of phosphorylation by kinases, phosphatases, ligands, and receptors, and downstream regulation.
° The bibliography contains a hyperlinked references relating specifically to this phosphorylation site that have been curated into PhosphoSite.

References:

  1. Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T, Subramaniam S. (2002). The Molecule Pages database. Nature. 420 ,716-7.

  2. Obenauer,J.C., Cantley,L.C., and Yaffe,M.B. (2003). Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31,3635.

  3. Protein Kinase Resource (PKR) http://pkr.sdsc.edu/html/index.shtml

  4. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. (2002) The Pfam protein families database. Nucleic Acids Res. 30:276.


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