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The tmRDB and SRPDB resources.

Ebbe Sloth Andersen1, Magnus Alm Rosenblad, Niels Larsen

  • 1Department of Molecular Biology, University of Aarhus, C.F. Moellers Allé, Building 139, 8000 Aarhus, Denmark.

Nucleic Acids Research
|December 31, 2005
PubMed
Summary
This summary is machine-generated.

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The tmRNA database (tmRDB) and signal recognition particle database (SRPDB) offer curated alignments of bacterial ribonucleoprotein complexes and proteins involved in protein targeting. These resources aid research into ribosome rescue and protein secretion pathways.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • The tmRNA-protein complex (tmRNP) rescues stalled bacterial ribosomes.
  • The signal recognition particle (SRP) targets secretory proteins to cell membranes.
  • Understanding these complexes is crucial for bacterial physiology and protein trafficking.

Purpose of the Study:

  • To provide curated databases for tmRNA and SRP.
  • To facilitate research on tmRNP and SRP structure and function.
  • To offer a centralized resource for comparative sequence analysis and structural data.

Main Methods:

  • Curated alignments of tmRNA and SRP RNA sequences.
  • Inclusion of associated protein sequences (SmpB, ribosomal protein S1, EF-Tu, SRP proteins, SRP receptors).

Related Experiment Videos

  • Development of an exploratory browser for examining alignments.

    • Main Results:

    • Established tmRDB and SRPDB with mirror sites for accessibility.
    • Provided curated alignments based on comparative sequence analysis.
    • Integrated links to high-resolution structures and molecular modeling data.

    Conclusions:

    • The tmRDB and SRPDB serve as valuable, accessible resources for researchers.
    • These databases support detailed investigations into tmRNP and SRP functions.
    • The integrated structural data enhances understanding of these essential molecular machines.