topPTM is a database that integrates experimentally verified post-translational modifications (PTMs) from available databases and research articles, and annotates the PTM sites on transmembrane proteins with structural topology. The biological effects of PTMs on transmembrane proteins include phosphorylation for signal transduction and ion transport, acetylation for structure stability, attachment of fatty acids for membrane anchoring and association, as well as the glycosylation for substrates targeting, cell-cell interactions, and viruses infection. The experimentally verified PTMs are mainly collected from public resources including dbPTM, Phospho.ELM, PhosphoSite, OGlycBase, and UbiProt. For transmembrane proteins, the information of membrane topologies is collected from TMPad, TOPDB, PDBTM, and OPM. In order to fully investigate the PTMs on transmembrane proteins, the UniProtKB protein entries containing the annotation of membrane protein and the information of membrane topology are regarded as potential transmembrane proteins. To delineate the structural correlation and consensus motif of these reported PTM sites, the topPTM database also provide structural analyses, including the membrane accessibility of PTM substrate sites, protein secondary and tertiary structures, protein domains, and cross-species conservations of each entry.
Highlight: A special case of Bacteriorhodopsin
( PDB ID: 1BM1) containing N6-(retinylidene)lysine on transmembrane region.
Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang, and Tzong-Yi Lee
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.
Nucl. Acids Res. (1 January 2014) 42 (D1): D537-D545 doi:10.1093/nar/gkt1221.[PubMed]