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UbSRD: The Ubiquitin Structural Relational Database.

Joseph S Harrison1, Tim M Jacobs2, Kevin Houlihan2

  • 1Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Journal of Molecular Biology
|September 23, 2015
PubMed
Summary
This summary is machine-generated.

The Ubiquitin Structural Relational Database (UbSRD) classifies ubiquitin-like protein structures. It reveals distinct interaction features for ubiquitin (UBQ) and SUMO, and the flexible UBQ tail conformation during binding.

Keywords:
RosettaSUMOprotein–protein interactionstructural databaseubiquitin

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Biochemistry

Background:

  • Ubiquitin-like (UBL) proteins mediate diverse protein-protein interactions.
  • High-resolution techniques have characterized many UBL complexes.
  • A comprehensive resource for analyzing UBL structural features is needed.

Purpose of the Study:

  • To create a database (UbSRD) for classifying and analyzing UBL-containing protein structures.
  • To define recognition features of ubiquitin (UBQ) and SUMO.
  • To investigate the conformational flexibility of the UBQ tail in protein interactions.

Main Methods:

  • Utilized Rosetta's structural classification tools to build the Ubiquitin Structural Relational Database (UbSRD).
  • Compiled features for 509 UBL-containing structures from the Protein Data Bank (PDB).
  • Enabled browsing by protein-protein interaction and quantitative structural analysis.

Main Results:

  • UbSRD provides a platform for analyzing UBL structural features and interactions.
  • Identified distinct recognition features for UBQ and SUMO, despite overlapping interaction surfaces.
  • Demonstrated that the UBQ tail is conformationally malleable upon binding.

Conclusions:

  • UbSRD facilitates the study of UBL protein-protein interactions and structural diversity.
  • Distinct features enable molecular discrimination between UBQ and SUMO.
  • The flexibility of the UBQ tail is a key aspect of its binding interactions.