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SRPDB (Signal Recognition Particle Database)
J Gorodkin1, B Knudsen, C Zwieb
1Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark.
Nucleic Acids Research
|January 11, 2000
Summary
The Signal Recognition Particle Database (SRPDB) is updated with new sequences for SRP RNA and proteins, enhancing its utility for studying protein translocation. This resource aids in identifying conserved elements and understanding SRP function in translation.
Area of Science:
- Molecular Biology
- Biochemistry
- Bioinformatics
Background:
- Signal Recognition Particle (SRP) is a crucial ribonucleoprotein complex for protein translocation across membranes during translation.
- Existing databases require updates to reflect new sequence data and improve accessibility for researchers.
Purpose of the Study:
- To update and expand the SRP Database (SRPDB) with new sequence data for SRP components and related proteins.
- To enhance the database's usability for computational analysis and research into protein targeting and translocation.
Main Methods:
- Compilation and organization of new SRP RNA and protein sequences.
- Phylogenetic analysis and alignment of sequences, highlighting conserved residues and base pairs.
- Inclusion of sequence motifs, RNA secondary structure diagrams, and 3D models for enhanced data visualization and analysis.
Main Results:
- The SRPDB now includes 129 SRP RNA sequences, 7 SRP9, 10 SRP14, 16 SRP19, 66 SRP54 (ffh), 7 SRP68, and 9 SRP72 sequences.
- Seven new SRP receptor alpha-subunit/FtsY homolog sequences (total 51) were added, along with other related proteins.
- Data are presented in user-friendly formats, including column arrangements and links to high-resolution structures.
Conclusions:
- The updated SRPDB provides a comprehensive and accessible resource for studying SRP function and evolution.
- Enhanced data presentation and computational tools facilitate further research into the mechanisms of protein translocation.