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Detailed analysis of RNA–protein interactions within the bacterial ribosomal protein L5/5S rRNA complex

Published online by Cambridge University Press:  16 January 2003

ANNA PEREDERINA
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
NATALIA NEVSKAYA
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
OLEG NIKONOV
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
ALEXEI NIKULIN
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
PHILIPPE DUMAS
Affiliation:
Unité Propre de Recherche 902 du Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg-cedex, France
MIN YAO
Affiliation:
Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
ISAO TANAKA
Affiliation:
Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
MARIA GARBER
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
GEORGE GONGADZE
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
STANISLAV NIKONOV
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
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Abstract

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 Å resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA–protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the β-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.

Type
Research Article
Information
RNA , Volume 8 , Issue 12 , December 2002 , pp. 1548 - 1557
Copyright
2002 RNA Society

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