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

RNA

Volumn 8, Issue 12, 2002, Pages 1548-1557

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

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^b INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

5S rRNA; Ribosomal protein L5; RNA protein interactions; Thermus thermophilus; X ray structure

Indexed keywords

NUCLEOTIDE; RIBOSOME PROTEIN; RIBOSOME RNA; RNA;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BETA SHEET; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GEOBACILLUS STEAROTHERMOPHILUS; HALOARCULA MARISMORTUI; HYDROGEN BOND; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA BINDING; THERMUS THERMOPHILUS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; ESCHERICHIA COLI; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; RIBOSOMAL PROTEINS; RNA, RIBOSOMAL, 5S;

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GEOBACILLUS STEAROTHERMOPHILUS; HALOARCULA; HALOARCULA MARISMORTUI; THERMUS; THERMUS THERMOPHILUS;

EID: 0036909186     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (28)

1. Bailey S. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D50:760-763.
2. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289:905-920.
3. Brunel C, Romby P, Westhof E, Ehresmann C, Ehresmann B. 1991. Three-dimensional model of Escherichia coli ribosomal 5S RNA as deduced from structure probing in solution and computer modeling. J Mol Biol 221:293-308.
4. Brünger AT, Adams PD, Marius Clore G, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu, NS, Read RJ, Rice LM, Simonson T, Warren GL. 1998. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D54:905-921.
5. Erdmann VA, Appel B, Digweed M, Kluwe D, Lorennz S, Luck A, Schreiber A, Schuster L. 1980. Structure and function of 5S and 5,8S ribosomal RNAs. In: Osawa S, Ozeki H, Uchida H, Yura T, eds., Genetics and Evolution of RNA Polymerase, tRNA and Ribosomes, Tokyo: University of Tokyo Press. pp 553-568.
6. Fedorov R, Meshcheryakov V, Gongadze G, Fomenkova N, Nevskaya N, Selmer M, Laurberg M, Kristensen Q, Al-Karadaghi S, Liljas A, Garber M, Nikonov S. 2001. Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins. Acta Crystallogr D57:968-976.
7. Gongadze GM, Perederina AA, Meshcheryakov VA, Fedorov RV, Moscalenko SE, Rak AV, Serganov AA, Shcherbakov DV, Nikonov SV, Garber MB. 2001. The Thermus thermophilus 5S rRNA-protein complex: Identification of specific binding sites for proteins L5 and L18 in the 5S rRNA. Mol Biol (Moscow) 35:521-526.
8. Gongadze GM, Tishchenko SV, Sedelnikova SE, Garber MB. 1993. Ribosomal proteins, TL4 and TL5, from Thermus thermophilus form hybrid complexes with 5S ribosomal RNA from different microorganisms. FEBS Lett 330:46-48.
9. Gourse RL, Thurlow DL, Gerbi SA, Zimmermann RA. 1981. Specific binding of a prokaryotic ribosomal protein to an eukaryotic ribosomal RNA: Implications for evolution and autoregulation. Proc Natl Acad Sci USA 78:2722-2726.
10. Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. 2001. High resolution structure of the large ribosomal subunit from mesophilic eubacterium. Cell 107:679-688.
11. Horne JR, Erdmann VA. 1972. Isolation and characterization of 5S RNA-protein complexes from Bacillus stearothermophilus and Escherichia coli ribosomes. Molec Gen Genet 119:337-344.
12. Jones TA, Zou J-Y, Cowan SW, Kjeldgaard M. 1991. Improved methods for the building of protein models in electron density maps and the location of errors in these. Acta Crystallogr A47:110-119.
13. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291.
14. Leontis NB, Westhof E. 1998. The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure. RNA 4:1134-1153.
15. Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512.
16. Meshcheryakov VA, Gryaznova OI, Davydova NL, Mudrik ES, Perederina AA, Vasilenko KS, Gongadze GM, Garber MB. 1997. RNA-binding properties of an unusual ribosomal protein TL5 from Thermus thermophilus. Biochemistry 62:629-634.
17. Nakashima T, Yao M, Kawamura S, Iwasaki K, Kimura M, Tanaka I. 2001. Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding. RNA 7:692-701.
18. Navaza J. 1994. AmoRe: An automated package for molecular replacement. Acta Crystallogr A50:157-163.
19. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. 2000. The structural basis of ribosomal activity in peptide bond synthesis. Science 289:920-930.
20. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA. 2001. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc Natl Acad Sci USA 98:4899-4903.
21. Noller HF. 1998. Ribosomal RNA. In: Simons RW, Grunberg-Manago M, eds. RNA Structure and Function. Plainview, New York: Cold Spring Harbor Laboratory Press. pp 73-92.
22. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
23. Sergiev P, Dokudovskaya S, Romanova E, Topin A, Bogdanov A, Brimacombe R, Dontsova O 0. 1998. The environment of 53 rRNA in the ribosome: Cross-links to the GTPase-associated area of 23S rRNA. Nucleic Acids Res 26:2511-2525.
24. Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. 2002. 5S ribosomal RNA database. Nucleic Acids Res 30:176-178.
25. Tishchenko S, Nikulin A, Fomenkova N, Nevskaya N, Nikonov O, Dumas P, Moine H, Ehresmann B, Ehresmann C, Piendl W, Lamzin V, Garber M, Nikonov S. 2001. Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeaon Methanococcus jannaschii. J Mol Biol 311:331-334.
26. Vysotskaya V, Tishchenko S, Garber M, Kern D, Mougel M, Ehresmann C, Ehresmann B. 1994. The ribosomal protein S8 from Thermus thermophilus VK1: Sequencing of the gene, expression of the protein in Escherichia coli and interaction with rRNA. Eur J Biochem 223:437-445.
27. Westhof E, Romby P, Romaniuk PJ, Ebel JP, Ehresmann C, Ehresmann B. 1989. Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5S rRNAs. J Mol Biol 207:417-431.
28. Yusupov MM, Yusupova GZh, Baucom A, Lieberman K, Earnest TN, Cate JHD, Noller HF. 2001. Crystal structure of the ribosome at 5.5 Å resolution. Science 292:883-896.