Structural motifs of the bacterial ribosomal proteins S20, S18 and S16 that contact rRNA present in the eukaryotic ribosomal proteins S25, S26 and S27A, respectively

Nucleic Acids Research

Volumn 38, Issue 6, 2009, Pages 2089-2098

  Malygin, Alexey A ^a   Karpova, Galina G ^a  

^a INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN S 16; PROTEIN S18; PROTEIN S20; RIBOSOME PROTEIN; RIBOSOME RNA; UNCLASSIFIED DRUG; RIBOSOMAL PROTEIN S18; RIBOSOMAL PROTEIN S20; RIBOSOMAL PROTEIN S27A;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEPLETION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS; THERMUS THERMOPHILUS; ANIMAL; CHEMISTRY; EUKARYOTE; GENETICS; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; SMALL RIBOSOMAL SUBUNIT;

BACTERIA (MICROORGANISMS); EUKARYOTA; THERMUS THERMOPHILUS;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; EUKARYOTA; MOLECULAR SEQUENCE DATA; RIBOSOMAL PROTEINS; RIBOSOME SUBUNITS, SMALL, BACTERIAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; THERMUS THERMOPHILUS;

EID: 77951223749     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1170     Document Type: Article

References (26)

1. Ramakrishnan, V. (2002) Ribosome structure and the mechanism of translation. Cell, 108, 557-572.
2. Brodersen, D.E., Clemons, W.M. Jr, Carter, A.P., Wimberly, B.T. and Ramakrishnan, V. (2002) Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA. J. Mol. Biol., 316, 725-768.
3. Lecompte, O., Ripp, R., Thierry, J.C., Moras, D. and Poch, O. (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res., 30, 5382-5390.
4. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
5. Gouet, P., Courcelle, E., Stuart, D.I. and Metoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics, 15, 305-308.
6. Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
7. Selmer, M., Dunham, C.M., Murphy, F.V. 4th, Weixlbaumer, A., Petry, S., Kelley, A.C., Weir, J.R. and Ramakrishnan, V. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science, 313, 1935-1942.
8. DeLano, W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.
9. Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M. et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
10. Lesk, A.M. (2004) Introduction to Protein Science: Architecture, Function, and Genomics. Oxford University Press, Oxford.
11. Yusupova, G., Jenner, L., Rees, B., Moras, D. and Yusupov, M. (2006) Structural basis for messenger RNA movement on the ribosome. Nature, 444, 391-394.
12. Schuwirth, B.S., Day, J.M., Hau, C.W., Janssen, G.R., Dahlberg, A.E., Cate, J.H. and Vila-Sanjurjo, A. (2006) Structural analysis of kasugamycin inhibition of translation. Nat. Struct. Mol. Biol., 13, 879-886.
13. Ban, N., Nissen, P., Hansen, J., Moore, P.B. and Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science, 289, 905-920.
14. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F. and Yonath, A. (2001) High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell, 107, 679-688.
15. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H. and Noller, H.F. (2001) Crystal structure of the ribosome at 5.5 Å resolution. Science, 292, 883-896.
16. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Bartels, H., Agmon, I. and Yonath, A. (2002) Protein structure: experimental and theoretical aspects. FEBS Lett., 525, 76-78.
17. Chandramouli, P., Topf, M., Menetret, J.F., Eswar, N., Cannone, J.J., Gutell, R.R., Sali, A. and Akey, C.W. (2008) Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure, 16, 535-548.
18. Graifer, D., Molotkov, M., Styazhkina, V., Demeshkina, N., Bulygin, K., Eremina, A., Ivanov, A., Laletina, E., Ven'yaminova, A. and Karpova, G. (2004) Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites. Nucleic Acids Res., 32, 3282-3293.
19. Malygin, A.A., Graifer, D.M., Bulygin, K.N., Zenkova, M.A., Yamkovoy, V.I., Stahl, J. and Karpova, G.G. (1994) Arrangement of mRNA at the decoding site of human ribosomes. 18S rRNA nucleotides and ribosomal proteins cross-linked to oligouridylate derivatives with alkylating groups at either the 3′ or the 5′ termini. Eur. J. Biochem., 226, 715-723.
20. Pisarev, A.V., Kolupaeva, V.G., Yusupov, M.M., Hellen, C.U. and Pestova, T.V. (2008) Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J., 27, 1609-1621.
21. Dontsova, O., Kopylov, A. and Brimacombe, R. (1991) The location of mRNA in the ribosomal 30S initiation complex; site-directed cross-linking of mRNA analogues carrying several photo-reactive labels simultaneously on either side of the AUG start codon. EMBO J., 10, 2613-2620.
22. Yusupova, G.Z., Yusupov, M.M., Cate, J.H. and Noller, H.F. (2001) The path of messenger RNA through the ribosome. Cell, 106, 233-241.
23. Marzi, S., Myasnikov, A.G., Serganov, A., Ehresmann, Ch., Romby, P., Yusupov, M. and Klaholz, B.P. (2007) Structured mRNAs regulate translation initiation by binding to the platform of the ribosome. Cell, 130, 1019-1031.
24. Pioletti, M., Schlünzen, F., Harms, J., Zarivach, R., Glühmann, M., Avila, H., Bashan, A., Bartels, H., Auerbach, T., Jacobi, C. et al. (2001) Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J., 20, 1829-1839.
25. Tolan, D.R., Hershey, J.W. and Traut, R.T. (1983) Crosslinking of eukaryotic initiation factor eIF3 to the 40S ribosomal subunit from rabbit reticulocytes. Biochimie, 65, 427-436.
26. Malygin, A.A., Shaulo, D.D. and Karpova, G.G. (2000) Proteins S7, S10, S16 and S19 of the human 40S ribosomal subunit are most resistant to dissociation by salt. Biochim. Biophys. Acta, 1494, 213-216.