Data in support of UbSRD: The Ubiquitin Structural Relational Database

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Ubiquitin-like (UBL) domains are crucial in biological processes, including post-translational modifications like ubiquitination (UBQ) and SUMOylation.
• These domains are involved in various protein-protein interactions (PPIs), essential for cellular functions.
• High-resolution structural data exists for many UBL domains, particularly UBQ and SUMO.

Purpose of the Study:

• To develop a comprehensive relational database, UbSRD, for analyzing UBL domain structures and interactions.
• To characterize quantitative properties of UBQ and SUMO recognition at different interface types (noncovalent, conjugated, deubiquitinase).
• To provide a resource for scientists studying the molecular basis of UBQ and SUMO recognition.

Main Methods:

• Identification and structural analysis of all UBL domains in the Protein Data Bank (PDB) using Rosetta software.
• Creation of the Ubiquitin Structural Relational Database (UbSRD).
• Utilizing PROMALS3D for multiple sequence alignment and phylogram construction of UBLs.

Main Results:

• UbSRD enables reporting of quantitative properties for UBQ and SUMO recognition.
• Detailed analysis of non-UBL neighbors, secondary structures of interacting motifs, and inter-molecular hydrogen bonds for UBQ and SUMO residues.
• A phylogram of UBLs was generated, illustrating evolutionary relationships.

Conclusions:

• The UbSRD database is a valuable resource for understanding UBL domain-mediated interactions.
• The reported data facilitates research into the molecular mechanisms of UBQ and SUMO recognition.
• This work supports the broader scientific community in studying protein modification and interaction networks.