STRUCTURAL STUDIES ON RIBISOMAL 5S RNA AND ITS FRAGMENTS
Ch. Betzel1, M.
Perbandt1, S. Lorenz2
and V.A. Erdmann2
1 Institute of
Physiological Chemistry, University Hamburg, c-o Desy Build. 22a, Notkestrasse 85,
20246 Hamburg, Germany
2 Instutute of
biochemistry, Free University Berlin, Thielallee 63, 14195
Berlin, Germany
Keywords: 5S rRNA, crystal
structure, RNA-RNA interaction, hairpin-loop
The ribisomal 5S RNA is approximately 120
nucleotides long and is an integral of the large ribosomal
subunit. Several parts of the 5S rRNA interact specifically with
several ribosomal proteins (1-3). It is clear that reconstituted
50S ribosomal subunits, lacking the 5S rRNA, are inactive in
proteinbiosynthesis. The function most drastically impaired is
that of the peptidyltransferase (1,2). Nevertheless, its precise
role in protein synthesis remains unclear. Structural studies
support a more detailed understanding of the 5S rRNA function.
Chemical probing as well as sequence alignment have permitted to
build a more general model for the 5S rRNA secondary
structure(4). Our extensive attempts to crystallize the entire
molecule have led to crystals which diffract only to moderate
resolution. So far a native data set has been collected any heavy
atom search is currently in preparation. To obtain information at
atomic resolution we have turned to the chemical synthesis (5),
crystallization and structure analysis of the various structural
domains applying synchrotron radiation. The molecular structures
of these parts of the 5S rRNA are one step to increase our
knowledge of how proteins recognise and interact with ribosomal
nucleic acids. Beside the X-ray structure of domain A, which
incorporates non Watson Crick base pairs, we will present the
structure of domain E. Domain E is of major interest because
crosslink between 5S rRNA and 23S rRNA demonstrated that the
location of the hairpin loop in domain E is near the
peptidyltransferase centre of the ribosome. The hairpin of domain
E belongs to the highly conserved class of very stable 5-GNRA
tetraloops occurring in ribosomal RNA which show different
sequences in different organism. This fact leads to the
assumption, that the conformation of the hairpin loop is also
different between the species. The conformation and interaction
of two molecules in the assymmetric unit give also some new hints
about RNA-RNA interactions as they might occur for instance in
the ribosome. The structure presented, as well as dynamic light
scattering and small angle X-ray scattering studies, demonstrate
the apparently large reservoir of structural flexibility of RNA
molecules.