PupDB: a database of pupylated proteins

BMC Bioinformatics. 2012 Mar 16;13:40. doi: 10.1186/1471-2105-13-40.

Abstract

Background: Prokaryotic ubiquitin-like protein (Pup), the firstly identified post-translational protein modifier in prokaryotes, is an important signal for the selective degradation of proteins. Recently, large-scale proteomics technology has been applied to identify a large number of pupylated proteins. The development of a database for managing pupylated proteins and pupylation sites is important for further analyses.

Description: 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.

Conclusions: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / chemistry
  • Bacteria / metabolism*
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Databases, Protein*
  • Internet
  • Protein Processing, Post-Translational*
  • Proteomics
  • Substrate Specificity
  • Ubiquitins / metabolism*

Substances

  • Bacterial Proteins
  • Ubiquitins