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PupDB: a database of pupylated proteins
1School of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan. cwtung@kmu.edu.tw
Pupylation, a prokaryotic post-translational modification, tags proteins for degradation. PupDB is a new database managing identified pupylated proteins and sites, aiding future research.
Area of Science:
- Biochemistry
- Proteomics
- Bioinformatics
Background:
- Prokaryotic ubiquitin-like protein (Pup) is the first identified post-translational modifier in prokaryotes.
- Pupylation signals selective protein degradation, with recent proteomics identifying numerous pupylated proteins.
- Managing pupylated proteins and sites is crucial for further research.
Purpose of the Study:
- To develop a comprehensive, web-based database for pupylated proteins and their modification sites.
- To facilitate the management and analysis of pupylation data.
- To support research into pupylation's role in prokaryotic systems.
Main Methods:
- PupDB was constructed by compiling experimentally verified pupylated proteins and sites from literature.
- Integrated data includes protein structures and functional annotations.
- The database offers browsing, searching, and interactive visualization tools.
Main Results:
- PupDB is a structured, searchable, web-based resource.
- It provides tools for exploring pupylated proteins and their modification sites.
- Includes integrated structural and functional information.
Conclusions:
- PupDB serves as a valuable resource for studying substrate specificity.
- It aids in identifying pupylated proteins across different organisms.
- Facilitates the development of computational tools for predicting pupylation sites.
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