title: Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.
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 A 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 beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia.
authors.forename: Anna
authors.initials: A
authors.lastname: Perederina
authors.forename: Natalia
authors.initials: N
authors.lastname: Nevskaya
authors.forename: Oleg
authors.initials: O
authors.lastname: Nikonov
authors.forename: Alexei
authors.initials: A
authors.lastname: Nikulin
authors.forename: Philippe
authors.initials: P
authors.lastname: Dumas
authors.forename: Min
authors.initials: M
authors.lastname: Yao
authors.forename: Isao
authors.initials: I
authors.lastname: Tanaka
authors.forename: Maria
authors.initials: M
authors.lastname: Garber
authors.forename: George
authors.initials: G
authors.lastname: Gongadze
authors.forename: Stanislav
authors.initials: S
authors.lastname: Nikonov
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D012341:RNA, Ribosomal, 5S / Q000737:chemistry* / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D010446:Peptide Fragments; D012341:RNA, Ribosomal, 5S; D012269:Ribosomal Proteins; C029742:ribosomal protein L5