Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC

Nucleic Acids Research

Volumn 35, Issue 13, 2007, Pages 4264-4274

  Sunita, S ^a   Purta, Elzbieta ^b,c   Durawa, Malgorzata ^b   Tkaczuk, Karolina L ^b,d   Swaathi, J ^a   Bujnicki, Janusz M ^b   Sivaraman, J ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^c INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

^d LODZ UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE; PROTEIN RSMC; RNA 16S; RNA METHYLTRANSFERASE; S ADENOSYLMETHIONINE; UNCLASSIFIED DRUG; AMINO ACID; ESCHERICHIA COLI PROTEIN; METHYLTRANSFERASE; RSMC PROTEIN, E COLI;

ARTICLE; BACTERIAL GENETICS; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME BINDING; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; RNA BINDING; RNA METABOLISM; SEQUENCE HOMOLOGY; AMINO ACID SEQUENCE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION;

ESCHERICHIA COLI;

AMINO ACID SEQUENCE; AMINO ACIDS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI PROTEINS; METHYLTRANSFERASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; S-ADENOSYLMETHIONINE; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 34547829268     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm411     Document Type: Article

References (51)

1. Loenen,W.A. (2006) S-adenosylmethionine: Jack of all trades and master of everything? Biochem. Soc. Trans., 34, 330-333.
2. Cheng,X. and Blumenthal,R.M. (1999) S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions. World Scientific Publishing, New Jersey.
3. Marinus,M.G. (1996) In Neihardt,F.C. (ed.), Escherichia coli and Salmonella typhimurium, 2nd edn. ASM Press, Washington DC, pp. 782-791.
4. Cheng,X. and Roberts,R.J. (2001) AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res., 29 3784-3795.
5. Pahlich,S., Zakaryan,R.P. and Gehring,H. (2006) Protein arginine methylation: Cellular functions and methods of analysis. Biochim. Biophys. Acta., 1764, 1890-1903.
6. Bujnicki,J.M., Droogmans,L., Grosjean,H., Purushothaman,S.K. and Lapeyre,B. (2004) In Bujnicki,J.M. (ed.), Practical Bioinformatics. Springer, Berlin, Vol. 15, pp. 139-168.
7. Rozenski,J., Crain,P.F. and McCloskey,J.A. (1999) The RNA modification database: 1999 update. Nucleic Acids Res., 27, 196-197.
8. Maden,B.E. and Hughes,J.M. (1997) Eukaryotic ribosomal RNA: The recent excitement in the nucleotide modification problem. Chromosoma, 105, 391-400.
9. Lapeyre,B. (2005) In Grosjean,H. (ed.), Fine-tuning of RNA Functions by Modification and Editing., Springer, Berlin, Heidelberg, Vol. 12.
10. Lee,T.T., Agarwalla,S. and Stroud,R.M. (2005) A unique RNA fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell, 120, 599-611.
11. Jemiolo,D.K., Taurence,J.S. and Giese,S. (1991) Mutations in 16S rRNA in Escherichia coli at methyl-modified sites: G966, C967, and G1207. Nucleic Acids Res., 19, 4259-4265.
12. Hendrickson,W.A. and Teeter,M.M. (1981) Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur. Nature, 290, 107-113.
13. Laskowski,R.A., MacArthur,M.W., Moss,D.S. and Thornton,J.M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
14. 2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. BMC Bioinformatics, 3 10.
15. Bujinicki,J.M. (2000) Phylogenomic analysis of 16S rRNA: (guanine-N 2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases. Faseb J., 14, 2365-2368.
16. Hohn,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
17. Kozbial,P.Z. and Mushegian,A.R. (2005) Natural history of S-adenosylmethionine-binding proteins. BMC Struct. Biol., 5, 19.
18. Sergiev,P.V., Lesnyak,D.V., Bogdanov,A.A. and Dontsova,O.A. (2006) Identification of Escherichia coli m2G methyltransferases: II. The ygjO gene encodes a methyltransferase specific for G1835 of the 23S rRNA. J. Mol. Biol., 364, 26-31.
19. Terribilini,M., Lee,J.H., Yan,C., Jernigan,R.L., Honavar,V. and Dobbs,D. (2006) Prediction of RNA binding sites in proteins from amino acid sequence. RNA, 12, 1450-1462.
20. Wang,L. and Brown,S.J. (2006) BindN: A web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., 34, W243-248.
21. Nallamsetty,S. and Waugh,D.S. (2006) Solubility-enhancing proteins MBP and NusA play a passive role in the folding of their fusion partners. Protein Expr. Purif., 45, 175-182.
22. Maravic,G., Bujnicki,J.M., Feder,M., Pongor,S. and Flogel,M. (2003) Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res., 31, 4941-4949.
23. Roth,C., Rastogi,S., Arvestad,L., Dittmar,K., Light,S., Ekman,D. and Liberles,D.A. (2006) Evolution after gene duplication: Models, mechanisms, sequences, systems, and organisms. J. Exp. Zool. B Mol. Dev. Evol., 308, 58-73.
24. Gille,C., Goede,A., Schloetelburg,C., Preissner,R., Kloetzel,P.M., Gobel,U.B. and Frommel,C. (2003) A comprehensive view on proteasomal sequences: Implications for the evolution of the proteasome. J. Mol. Biol., 326, 1437-1448.
25. Gerber,A.P. and Keller,W. (1999) An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science, 286, 1146-1149.
26. 1A58 methyltransferase family: Homology-based fold prediction and identification of new members from Eubacteria and Archaea. FEBS Lett. 507, 123-127.
27. 1A) methyltransferase. Nucleic Acids Res., 32, 465-476.
28. Gros,L., Renodon-Corniere,A., de Saint Vincent,B.R., Feder,M., Bujnicki,J.M. and Jacquemin-Sablon,A. (2006) Characterization of prmt7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors. Biochim. Biophys. Acta, Epub 2006 Sep 14, 1646-1656.
29. Gowher,H., Liebert,K., Hermann,A., Xu,G. and Jeltsch,A. (2005) Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J. Biol. Chem., 280, 13341-13348.
30. Kareta,M.S., Botello,Z.M., Ennis,J.J., Chou,C. and Chedin,F. (2006) Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L. J. Biol. Chem., Epub 2006 Jul 7, 25893-2590.
31. Lesnyak,D.V., Sergiev,P.V., Bogdanov,A.A. and Dontsova,O.A. (2006) Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. J. Mol. Biol., 364, 20-25.
32. Lesnyak,D.V., Osipiuk,J., Skarina,T., Sergiev,P.V., Bogdanov,A.A., Edwards,A., Savchenko,A., Joachimiak,A. and Dontsova,O.A. (2001) Methyltranferase that modifies guanine 966 of the 16S rRNA: Functional identification and tertiary structure. J. Biol. Chem., 282, 5880-5887.
33. Tscherne,J.S., Nurse,K., Popienick,P. and Ofengand,J. (1999) Purification, cloning, and characterization of the 16S RNA m2G1207 methyltransferase from Escherichia coli. J. Biol. Chem., 274 924-929.
34. Sergiev,P.V., Bogdanov,A.A. and Dontsova,O.A. (2007) Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Nucleic Acids Res. 35, 2295-2301.
35. Weitzmann,C., Tumminia,S.J., Boublik,M. and Ofengand,J. (1991) A paradigm for local conformational control of function in the ribosome: binding of ribosomal protein S19 to Escherichia coli 16S rRNA in the presence of S7 is required for methylation of m2G96 and blocks methylation of m5C967 by their respective methyltransferases. Nucleic Acids Res., 19, 7089-7095.
36. LeMaster,D.M. and Richards,F.M. (1985) 1H-15N heteronuclear NMR studies of Escherichis. coli thioredoxin in samples isotopically labeled by residue type. Biochemistry, 24, 7263-7268.
37. Daigle,D.M. and Brown,E.D. (2004) Studies of the interaction of Escherichia coli YjeQ with the ribosome in vitro. J. Bacteriol., 186, 1381-1387.
38. Matthews,B.W. (1968) Solvent content of protein crystals. J. Mol. Biol., 33, 491-497.
39. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
40. Terwilliger,T.C. and Berendzen,J. (1999) Automated MAD and MIR structure solution. Acta Crystallogr. D. Biol. Crystallogr., 55, 849-861.
41. Bricogne,G., Vonrhein,C., Flensburg,C., Schiltz,M. and Paciorek,W. (2003) Generation, representation and flow of phase information in structure determination: Recent developments in and around SHARP 2.0. Acta Crystallogr. D Biol. Crystallogr., 59, 2023-2030.
42. Perrakis,A., Morris,R. and Lamzin,V.S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol., 6, 458-463.
43. Jones,T.A., Zou,J.Y., Cowan,S.W. and Kjeldgaard,M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A, 47 Pt 2), 110-119.
44. Brunger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P., Grosse-Kunstleve,R.W., Jiang,J.S., Kuszewski,J., Nilges,M. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr., 54(Pt 5), 905-921.
45. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
46. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
47. Glaser,F., Pupko,T., Paz,I., Bell,R.E., Becher-Shental,D., Martz,E. and Ben-Tal,N. (2003) ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
48. Kraulis,J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst., 24, 946-950.
49. Merritt,E.A. and Murphy,M.E. (1994) Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D Biol. Crystallogr., 50, 869-873.
50. Kitagawa,M., Ara,T., Arifuzzaman,M., Ioka-Nakamichi,T., Inamoto,E., Toyonaga.H. and Mori,H. (2006) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res., 12, 291-299.
51. Baba,T., Ara,T., Hasegawa,M., Takai.Y., Okumura,Y., Baba,M., Datsenko,K.A., Tomita,M., Wanner,B.L. and Mori,H. (2006) Construction of Escherichia. coli-K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol, 2, 2006.0008.