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

Anna Perederina, Natalia Nevskaya, Oleg Nikonov, Alexei Nikulin, Philippe Dumas, Min Yao, Isao Tanaka, Maria Garber, George Gongadze, Stanislav Nikonov

Research output: Contribution to journalArticle

23 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1548-1557
Number of pages10
JournalRNA
Volume8
Issue number12
StatePublished - Dec 1 2002

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Bacterial Proteins
RNA
Thermus thermophilus
Proteins
Haloarcula marismortui
Membrane Proteins
Geobacillus stearothermophilus
Ribosome Subunits
Archaea
ribosomal protein L5
Hydrogen
Nucleotides
Escherichia coli
Bacteria

All Science Journal Classification (ASJC) codes

  • Molecular Biology

Cite this

Perederina, A., Nevskaya, N., Nikonov, O., Nikulin, A., Dumas, P., Yao, M., ... Nikonov, S. (2002). Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex. RNA, 8(12), 1548-1557.
Perederina, Anna ; Nevskaya, Natalia ; Nikonov, Oleg ; Nikulin, Alexei ; Dumas, Philippe ; Yao, Min ; Tanaka, Isao ; Garber, Maria ; Gongadze, George ; Nikonov, Stanislav. / Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex. In: RNA. 2002 ; Vol. 8, No. 12. pp. 1548-1557.
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Perederina, A, Nevskaya, N, Nikonov, O, Nikulin, A, Dumas, P, Yao, M, Tanaka, I, Garber, M, Gongadze, G & Nikonov, S 2002, 'Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex', RNA, vol. 8, no. 12, pp. 1548-1557.

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex. / Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav.

In: RNA, Vol. 8, No. 12, 01.12.2002, p. 1548-1557.

Research output: Contribution to journalArticle

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AU - Perederina, Anna

AU - Nevskaya, Natalia

AU - Nikonov, Oleg

AU - Nikulin, Alexei

AU - Dumas, Philippe

AU - Yao, Min

AU - Tanaka, Isao

AU - Garber, Maria

AU - Gongadze, George

AU - Nikonov, Stanislav

PY - 2002/12/1

Y1 - 2002/12/1

N2 - 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.

AB - 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.

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Perederina A, Nevskaya N, Nikonov O, Nikulin A, Dumas P, Yao M et al. Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex. RNA. 2002 Dec 1;8(12):1548-1557.