PupDB: a database of pupylated proteins

A database named PupDB is constructed by collecting experimentally identified pupylated proteins and pupylation sites from published studies and integrating the information of pupylated proteins with corresponding structures and functional annotations. PupDB is a web-based database with tools for browses and searches of pupylated proteins and interactive displays of protein structures and pupylation sites.The structured and searchable database PupDB is expected to provide a useful resource for further analyzing the substrate specificity, identifying pupylated proteins in other organisms and developing computational tools for predicting pupylation sites. PupDB is freely available at http://cwtung.kmu.edu.tw/pupdb webcite.Protein-to-protein modifications are essential for regulating protein functions. In eukaryotes, ubiquitylation involved in numerous regulatory functions such as protein degradation, DNA repair, transcription and signal transduction is particular important [1]. Recently, pupylation has been identified as the first post-translational protein-to-protein modification in prokaryotes [2,3]. Similar to ubiquitin, prokaryotic ubiquitin-like protein (Pup) attaches to specific lysine residues of substrate proteins by forming isopeptide bonds to target the proteins for proteasomal degradation [2,3].Although ubiquitylation and pupylation are functional analogues, the enzymology of ubiquitylation and pupylation is different. In contrast to the three-step reaction of ubiquitylation, pupylation requires only two steps that only two enzymes are involved in pupylation. First, the C-terminal glutamine of Pup is deamidated to glutamine by deamidase of Pup (Dop) [4]. Subsequently, proteasome accessory factor A (PafA) attaches the deamidated Pup to specific lysine residues of substrate proteins [5].The identification of pupylated proteins and pupylation sites can provide insights into the substrate specificity and functions of pupylation. Recently, large-scale proteomics