Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase

RNA

Volumn 13, Issue 7, 2007, Pages 967-973

  Walbott, Hélène ^a   Husson, Clotilde ^a,b   Auxilien, Sylvie ^a   Golinelli Pimpaneau, Béatrice ^a  

^a LABORATOIRE D ENZYMOLOGIE ET BIOCHIMIE STRUCTURALES   (France)

^b CNRS   (France)

Author keywords

5 fluorocytosine; Cysteine nucleophile; m 5C; RNA methyltransferase; Trm4

Indexed keywords

CYSTEINE; CYTOSINE; FLUCYTOSINE; FUNGAL ENZYME; MUTANT PROTEIN; RNA DERIVATIVE; S ADENOSYLMETHIONINE; TRANSFER RNA; TRANSFER RNA METHYLTRANSFERASE;

AMINO ACID SEQUENCE; ARTICLE; COVALENT BOND; ENZYME ACTIVE SITE; ENZYME STABILITY; ESCHERICHIA COLI; PRIORITY JOURNAL; PROTEIN MOTIF; RNA METHYLATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AMINO ACID MOTIFS; BASE SEQUENCE; CATALYSIS; CELL NUCLEUS; CYSTEINE; FLUCYTOSINE; METHYLATION; MODELS, BIOLOGICAL; MUTANT PROTEINS; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRNA METHYLTRANSFERASES;

ESCHERICHIA COLI;

EID: 34250876436     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.515707     Document Type: Article

References (30)

1. Agris, P.F. 2004. Decoding the genome: A modified view. Nucleic Acids Res. 32: 223-238.
2. 5U methyltransferases. Nucleic Acids Res. 32: 2453-2463.
3. Carreras, C.W. and Santi, D.V. 1995. The catalytic mechanism and structure of thymidylate synthase. Annu. Rev. Biochem. 64: 721-762.
4. Chen, L., MacMillan, A.M., Chang, W., Ezaz-Nikpay, K., Lane, W.S., and Verdine, G.L. 1991. Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase. Biochemistry 30: 11018-11025.
5. Dunin-Horkawicz, S., Czerwoniec, A., Gajda, M.J., Feder, M., Grosjean, H., and Bujnicki, J.M. 2006. MODOMICS: A database of RNA modification pathways. Nucleic Acids Res. 34: D145-D149.
6. England, T.E., Bruce, A.G., and Uhlenbeck, O.C. 1980. Specific labeling of 3′ termini of RNA with T4 RNA ligase. Methods Enzymol. 65: 65-74.
7. 5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure 11: 1609-1620.
8. Grosjean, H. 2005. Fine-tuning of RNA functions by modification and editing. Springer, Berlin.
9. Grosjean, H., Droogmans, L., Giege, R., and Uhlenbeck, O.C. 1990. Guanosine modifications in runoff transcripts of synthetic transfer RNA-Phe genes microinjected into Xenopus oocytes. Biochim. Biophys. Acta 1050: 267-273.
10. 5U54)-methyltransferase and RNA substrates. Biochemistry 31: 10295-10302.
11. Gu, X., Liu, Y., and Santi, D.V. 1999. The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA. Proc. Natl. Acad. Sci. 96: 14270-14275.
12. 5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. J. Mol. Biol. 360: 774-787.
13. Hoang, C. and Ferre-D'Amare, A.R. 2001. Cocrystal structure of a tRNA Psi55 pseudouridine synthase: Nucleotide flipping by an RNA-modifying enzyme. Cell 107: 929-939.
14. Hong, B., Brockenbrough, J.S., Wu, P., and Aris, J.P. 1997. Nop2p is required for pre-rRNA processing and 60S ribosome subunit synthesis in yeast. Mol. Cell. Biol. 17: 378-388.
15. Huang, L., Pookanjanatavip, M., Gu, X., and Santi, D.V. 1998. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry 37: 344-351.
16. Ishikawa, I., Sakai, N., Tamura, T., Yao, M., Watanabe, N., and Tanaka, I. 2004. Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii. Proteins 54: 814-816.
17. Ivanetich, K.M. and Santi, D.V. 1992. 5,6-Dihydropyrimidine adducts in the reactions and interactions of pyrimidines with proteins. Prog. Nucleic Acid Res. Mol. Biol. 42: 127-156.
18. 5U54)methyltransferase. Biochemistry 30: 9724-9728.
19. 5U54)methyltransferase. Biochimie 76: 1133-1142.
20. King, M.Y. and Redman, K.L. 2002. RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine. Biochemistry 41: 11218-11225.
21. King, M., Ton, D., and Redman, K.L. 1999. A conserved motif in the yeast nucleolar protein Nop2p contains an essential cysteine residue. Biochem. J. 337: 29-35.
22. 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.
23. 5C DNA methyl transferases use different cysteine residues as catalysts. Proc. Natl. Acad. Sci. 97: 8263-8265.
24. 5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme. RNA 5: 1105-1118.
25. Pan, H., Agarwalla, S., Moustakas, D.T., Finer-Moore, J., and Stroud, R.M. 2003. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc. Natl. Acad. Sci. 100: 12648-12653.
26. Redman, K.L. 2006. Assembly of protein-RNA complexes using natural RNA and mutant forms of an RNA cytosine methyltransferase. Biomacromolecules 7: 3321-3326.
27. 5C methyltransferases from searching genomic and proteomic sequences. Nucleic Acids Res. 27: 3138-3145.
28. Rozenski, J., Crain, P.F., and McCloskey, J.A. 1999. The RNA Modification Database: 1999 update. Nucleic Acids Res. 27: 196-197.
29. Sprinzl, M. and Vassilenko, K.S. 2005. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 33: D139-D140.
30. Wu, K., Wu, P., and Aris, J.P. 2001. Nucleolar protein Nop12p participates in synthesis of 25S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res. 29: 2938-2949.