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The signal recognition particle database (SRPDB)

N Larsen1, C Zwieb

  • 1Department of Microbiology, University of Illinois, Urbana 61801.

Nucleic Acids Research
|July 1, 1993
PubMed
Summary
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The Signal Recognition Particle Database (SRPDB) now includes 64 annotated SRP RNA sequences from Eukaryotes, Archaea, and bacteria, featuring comparative sequence analysis for RNA secondary structures and protein binding sites.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • The Signal Recognition Particle (SRP) system is crucial for targeting proteins to cellular membranes.
  • Understanding SRP RNA evolution and structure is key to deciphering protein targeting mechanisms.

Purpose of the Study:

  • To update and expand the Signal Recognition Particle Database (SRPDB) with new sequences and structural information.
  • To provide a comprehensive resource for studying SRP RNA and its interactions.

Main Methods:

  • Comparative sequence analysis of SRP RNA from Eukaryotes, Archaea, and bacteria.
  • Phylogenetic ordering and alignment of sequences.
  • Determination of RNA secondary structures and protein binding sites.

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Main Results:

  • The SRPDB now contains 64 annotated SRP RNA sequences, an increase of 17 from the previous release.
  • Representative RNA secondary structure diagrams are available, with base pairs validated by comparative analysis.
  • Alignments of SRP19 and SRP54 proteins, including their RNA binding sites, have been added.

Conclusions:

  • The updated SRPDB offers a valuable, phylogenetically organized resource for researchers studying SRP RNA and protein interactions.
  • The inclusion of structural and binding site data enhances the utility of SRPDB for functional and evolutionary studies.