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MESPEUS: a database of metal coordination groups in proteins
Geng-Yu Lin1, Yu-Cheng Su1, Yen Lin Huang1
1Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan.
Nucleic Acids Research
|November 9, 2023
Summary
MESPEUS is a new database detailing metal coordination geometry in metalloproteins. It offers a user-friendly interface for exploring metal sites, aiding research in structural biology and metalloprotein function.
Area of Science:
- Structural Biology
- Bioinorganic Chemistry
- Bioinformatics
Background:
- Metalloproteins play crucial roles in biological systems.
- Understanding metal coordination geometry is vital for elucidating protein function.
- Existing databases may lack comprehensive geometric details of metal sites.
Purpose of the Study:
- To develop MESPEUS, a freely accessible database of metal coordination groups in metalloprotein structures.
- To provide detailed geometrical information on metal sites, including 40 metal types.
- To facilitate the exploration of metal site characteristics through a user-friendly interface.
Main Methods:
- Extraction of metal coordination groups from Protein Data Bank (PDB) structures.
- Inclusion of symmetry-related units using space group operations for complete coordination description.
- Development of a web interface for searching and visualizing metal site data.
- Monthly synchronization with the PDB database for up-to-date information.
Main Results:
- MESPEUS contains geometrical data for metal sites across diverse metalloproteins.
- The database supports searches based on metal type, coordination number, donor residues, and structural resolution.
- Interactive visualization tools allow detailed examination of metal sites and their structural context.
- A case study demonstrates MESPEUS's utility in analyzing Mg-ATP interactions.
Conclusions:
- MESPEUS provides a valuable resource for researchers studying metalloproteins and metal coordination.
- The database enhances the understanding of metal site geometry and its impact on protein function.
- Its comprehensive data and intuitive interface streamline the investigation of metal-protein interactions.
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