Molecular basis for bacterial class I release factor methylation by PrmC

Molecular Cell

Volumn 20, Issue 6, 2005, Pages 917-927

  Graille, Marc ^a   Heurgué Hamard, Valérie ^b   Champ, Stéphanie ^b,c   Mora, Liliana ^b   Scrima, Nathalie ^b   Ulryck, Nathalie ^a   Van Tilbeurgh, Herman ^a   Buckingham, Richard H ^b  

^a INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^b INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^c CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; GLUTAMINE; PEPTIDE; PEPTIDYLTRANSFERASE; PROTEIN PRMC; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; EUKARYOTE; HYDROLYSIS; METHYLATION; MUTAGENESIS; NONHUMAN; PROKARYOTE; RIBOSOME; STOP CODON;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CODON, TERMINATOR; CRYSTALLOGRAPHY, X-RAY; DNA MUTATIONAL ANALYSIS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; METHYLATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIPROTEIN COMPLEXES; PEPTIDE TERMINATION FACTORS; PROTEIN CONFORMATION; PROTEIN METHYLTRANSFERASES; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

EID: 29144491478     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2005.10.025     Document Type: Article

References (40)

1. S. Bailey The CCP4 suite - programs for protein crystallography Acta Cryst. D50 1994 760 763
2. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54 1998 905 921
3. S. Clarke Protein methylation Curr. Opin. Cell Biol. 5 1993 977 983
4. V. Dinçbas, V. Heurgué-Hamard, R.H. Buckingham, R. Karimi, and M. Ehrenberg Shutdown in protein synthesis due to the expression of mini-genes in bacteria J. Mol. Biol. 291 1999 745 759
5. V. Dinçbas-Renqvist, Å. Engström, L. Mora, V. Heurgué-Hamard, R.H. Buckingham, and M. Ehrenberg A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation EMBO J. 19 2000 6900 6907
6. D.V. Freistroffer, M.Y. Pavlov, J. MacDougall, R.H. Buckingham, and M. Ehrenberg Release factor RF3 in E. coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP dependent manner EMBO J. 16 1997 4126 4133
7. L.Y. Frolova, R.Y. Tsivkovskii, G.F. Sivolobova, N.Y. Oparina, O.I. Serpinsky, V.M. Blinov, S.I. Tatkov, and L.L. Kisselev Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis RNA 5 1999 1014 1020
8. P. Gouet, E. Courcelle, D.I. Stuart, and F. Metoz ESPript: analysis of multiple sequence alignments in PostScript Bioinformatics 15 1999 305 308
9. V. Heurgué-Hamard, S. Champ, Å. Engstöm, M. Ehrenberg, and R.H. Buckingham The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors EMBO J. 21 2002 769 778
10. V. Heurgué-Hamard, S. Champ, L. Mora, T. Merkulova-Rainon, L.L. Kisselev, and R.H. Buckingham The glutamine residue of the conserved GGQ motif in Saccharomyces cerevisiae release factor eRF1 is methylated by the product of the YDR140w gene J. Biol. Chem. 280 2005 2439 2445
11. K. Ito, M. Uno, and Y. Nakamura A tripepeptide anticodon deciphers stop codons in messenger RNA Nature 403 2000 680 684
12. W. Kabsch Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants J. Appl. Crystallogr. 26 1993 795 800
13. L.L. Kisselev, and R.H. Buckingham Translational termination comes of age Trends Biochem. Sci. 25 2000 561 566
14. L.L. Kisselev, N.Y. Oparina, and L.Y. Frolova Class-1 translation termination factors are structurally and functionally similar to suppressor tRNAs and belong to distinct structural/functional families (prokaryotes/ mitochondria and eukaryotes/archaea) Mol. Biol. (Moscow) 34 2000 427 442
15. B.P. Klaholz, T. Pape, A.V. Zavialov, A.G. Myasnikov, E.V. Orlova, B. Vestergaard, M. Ehrenberg, and M. Van Heel Structure of the Escherichia coli ribosomal termination complex with release factor 2 Nature 421 2003 90 94
16. A.V. Kononenko, K.A. Dembo, L.L. Kisselev, and V.V. Volkov Molecular morphology of class-1 translation termination factor eRF1 in solution Mol. Biol. (Mosk.) 38 2004 303 311
17. U.K. Laemmli Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 227 1970 680 685
18. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
19. J. Lhoest, and C. Colson Genetics of ribosomal protein methylation in Escherichia coli. II. A mutant lacking a new type of methylated amino acid, N5-methylglutamine, in protein L3 Mol. Gen. Genet. 154 1977 175 180
20. L. Lo Conte, C. Chothia, and J. Janin The atomic structure of protein-protein recognition sites J. Mol. Biol. 285 1999 2177 2198
21. J. Lopilato, S. Bortner, and J. Beckwith Mutations in a new chromosomal gene of Escherichia coli K12, pcnB, reduces plasmid copy number of pBR322 and its derivatives Mol. Gen. Genet. 205 1986 285 290
22. B.W. Matthews Solvent content of protein crystals J. Mol. Biol. 33 1968 491 497
23. I.K. McDonald, and J.M. Thornton Satisfying hydrogen bonding potential in proteins J. Mol. Biol. 238 1994 777 793
24. L. Mora, A.V. Zavialov, M. Ehrenberg, and R.H. Buckingham Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli Mol. Microbiol. 50 2003 1467 1476
25. K. Nakahigashi, N. Kubo, S. Narita, T. Shimaoka, S. Goto, T. Oshima, H. Mori, M. Maeda, C. Wada, and H. Inokuchi HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination Proc. Natl. Acad. Sci. USA 99 2002 1473 1478
26. T. Nakayashiki, K. Nishimura, and H. Inokuchi Cloning and sequencing of a previously unidentified gene that is involved in the biosynthesis of heme in Escherichia coli Gene 153 1995 67 70
27. M.Y. Pavlov, D.V. Freistroffer, V. Dincbas, J. MacDougall, R.H. Buckingham, and M. Ehrenberg A direct estimation of the context effect on the efficiency of termination J. Mol. Biol. 284 1998 579 590
28. U.B. Rawat, A.V. Zavialov, J. Sengupta, M. Valle, R.A. Grassucci, J. Linde, B. Vestergaard, M. Ehrenberg, and J. Frank A cryo-electron microscopic study of ribosome-bound termination factor RF2 Nature 421 2003 87 90
29. M. Roth, S. Helm-Kruse, T. Friedrich, and A. Jeltsch Functional roles of conserved amino acid residues in DNA methyltransferases investigated by site-directed mutagenesis of the EcoRV adenine-N6-methyltransferase J. Biol. Chem. 273 1998 17333 17342
30. A. Roussel, and C. Cambillau Silicon Graphics Partners Directory 1989 Silicon Graphics Mountain View, CA pp. 77-79
31. M. Ryden, J. Murphy, L. Isaksson, and J. Gallant Mapping and complementation studies of the gene for release factor 1 J. Bacteriol. 168 1986 1066 1069
32. S.M. Ryden, and L.A. Isaksson A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors Mol. Gen. Genet. 193 1984 38 45
33. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular Cloning: A Laboratory Manual 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
34. H.L. Schubert, J.D. Phillips, and C.P. Hill Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase Biochemistry 42 2003 5592 5599
35. D.H. Shin, J. Brandsen, J. Jancarik, H. Yokota, R. Kim, and S.H. Kim Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome J. Mol. Biol. 341 2004 227 239
36. H. Song, P. Mugnier, A.K. Das, H.M. Webb, D.R. Evans, M.F. Tuite, B.A. Hemmings, and D. Barford The crystal structure of human eukaryotic release factor eRF1 - mechanism of stop codon recognition and peptidyl-tRNA hydrolysis Cell 100 2000 311 321
37. A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallogr. 30 1997 1022 1025
38. B. Vestergaard, L. Bich Van, G.R. Andersen, J. Nyborg, R.H. Buckingham, and M. Kjeldgaard Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1 Mol. Cell 8 2001 1375 1382
39. B. Vestergaard, S. Sanyal, M. Roessle, L. Mora, R.H. Buckingham, J.S. Kastrup, M. Gajhede, D.I. Svergun, and M. Ehrenberg The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure Mol. Cell 20 2005 929 938 this issue
40. Z. Yang, L. Shipman, M. Zhang, B.P. Anton, R.J. Roberts, and X. Cheng Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase J. Mol. Biol. 340 2004 695 706