The handling of the mechanistic probe 5-fluorouridine by the pseudouridine synthase truA and its consistency with the handling of the same probe by the pseudouridine synthases TruB and RluA

Biochemistry

Volumn 50, Issue 3, 2011, Pages 426-436

  McDonald, Marguerite K ^a   Miracco, Edward J ^a   Chen, Junjun ^a   Xie, Yizhou ^b   Mueller, Eugene G ^b  

^a UNIVERSITY OF DELAWARE   (United States)

^b UNIVERSITY OF LOUISVILLE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ASPARTIC ACIDS; DIGESTION PRODUCTS; DINUCLEOTIDES; ESTER HYDROLYSIS; HYDRATED PRODUCT; MECHANISTIC PROBES; MICHAEL ADDITIONS; PSEUDOURIDINE; PSEUDOURIDINE SYNTHASES; PYRIMIDINE RING; SYNTHASES;

ADDITION REACTIONS; AMINO ACIDS; ESTERIFICATION; ESTERS; HYDRATES; HYDROLYSIS; ORGANIC ACIDS; PROBES; RNA;

HYDRATION;

DINUCLEOTIDE; ESTER; FLUOROURIDINE; NUCLEOPHILE; NUCLEOSIDE; PROTEIN RLUA; PROTEIN TRUA; PSEUDOURIDINE; PSEUDOURIDINE SYNTHASE; RNA; SYNTHETASE; TRANSFER RNA; UNCLASSIFIED DRUG; URIDINE TRIPHOSPHATE;

ARTICLE; COMPLEX FORMATION; ELECTROSPRAY MASS SPECTROMETRY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROLYSIS; ISOMER; ISOTOPE LABELING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; RNA ADDUCT; RNA SYNTHESIS;

ASPARTIC ACID; ESCHERICHIA COLI PROTEINS; ESTERS; HYDROLYSIS; INTRAMOLECULAR TRANSFERASES; MOLECULAR PROBES; NUCLEOSIDES; RNA; URIDINE;

EID: 78751557887     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101737z     Document Type: Article

References (21)

1. Mueller, E. G. and Ferré-D'Amaré, A. R. (2009) Pseudouridine formation, the most common transglycosylation in RNA, in DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution (Grosjean, H., Ed.) pp 363 - 376, Landes Bioscience, Austin, TX.
2. Huang, L. X., Pookanjanatavip, M., Gu, X. G., 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
3. Ramamurthy, V., Swann, S. L., Paulson, J. L., Spedaliere, C. J., and Mueller, E. G. (1999) Critical aspartic acid residues in pseudouridine syntheses J. Biol. Chem. 274, 22225-22230
4. Raychaudhuri, S., Conrad, J., Hall, B. G., and Ofengand, J. (1998) A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli RNA 4, 1407-1417
5. Conrad, J., Niu, L. H., Rudd, K., Lane, B. G., and Ofengand, J. (1999) 16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: Deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases RNA 5, 751-763
6. Kaya, Y. and Ofengand, J. (2003) A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya RNA 9, 711-721
7. Gu, X. R., Liu, Y. Q., and Santi, D. V. (1999) The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA Proc. Natl. Acad. Sci. U.S.A. 96, 14270-14275
8. Hoang, C. and Ferré-D'Amaré, A. R. (2001) Cocrystal structure of a tRNA 55 pseudouridine synthase: Nucleotide flipping by an RNA-modifying enzyme Cell 107, 929-939
9. Spedaliere, C. J. and Mueller, E. G. (2004) Not all pseudouridine synthases are potently inhibited by RNA containing 5-fluorouridine RNA 10, 192-199
10. Spedaliere, C. J., Ginter, J. M., Johnston, M. V., and Mueller, E. G. (2004) The pseudouridine synthases: Revisiting a mechanism that seemed settled J. Am. Chem. Soc. 126, 12758-12759
11. Hoang, C., Chen, J. J., Vizthum, C. A., Kandel, J. M., Hamilton, C. S., Mueller, E. G., and Ferre-D'Amare, A. R. (2006) Crystal structure of pseudouridine synthase RluA: Indirect sequence readout through protein-induced RNA structure Mol. Cell 24, 535-545
12. Hamilton, C. S., Greco, T. M., Vizthum, C. A., Ginter, J. M., Johnston, M. V., and Mueller, E. G. (2006) Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine Biochemistry 45, 12029-12038
13. Darlix, J. L., Fromageot, H. P. M., and Fromageot, P. (1967) An improved method for the preparation of 52-monophosphoderivatives of the common ribonucleosides Biochim. Biophys. Acta 145, 517-519
14. Tolbert, T. J. and Williamson, J. R. (1996) Preparation of specifically deuterated RNA for NMR studies using a combination of chemical and enzymatic synthesis J. Am. Chem. Soc. 118, 7929-7940
15. Phannachet, K., Elias, Y., and Huang, R. H. (2005) Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase Biochemistry 44, 15488-15494
16. Gu, X. R., Yu, M., Ivanetich, K. M., and Santi, D. V. (1998) Molecular recognition of tRNA by tRNA pseudouridine 55 synthase Biochemistry 37, 339-343
17. Weinfeld, M., Liuzzi, M., and Paterson, M. C. (1989) Selective hydrolysis by exonucleases and endonucleases of phosphodiester bonds adjacent to an apurinic site Nucleic Acids Res. 17, 3735-3745
18. Weinfeld, M., Soderlind, K. J. M., and Buchko, G. W. (1993) Influence of nucleic acid base aromaticity on substrate reactivity with enzymes acting on single-stranded DNA Nucleic Acids Res. 21, 621-626
19. Visser, G. W. M., Herder, R. E., Noordhuis, P., Zwaagstra, O., Herscheid, J. D. M., and Dekanter, F. J. J. (1988) Reaction of acetyl hypofluorite with pyrimidines. 3. Synthesis, stereochemistry, and properties of 5-fluoro-5,6-dihydropyrimidine nucleosides J. Chem. Soc., Perkin Trans. 1, 2547-2554
20. Hamilton, C. S., Spedaliere, C. J., Ginter, J. M., Johnston, M. V., and Mueller, E. G. (2005) The roles of the essential Asp-48 and highly conserved His-43 elucidated by the pH dependence of the pseudouridine synthase TruB Arch. Biochem. Biophys. 433, 322-334
21. Mueller, E. G., Buck, C. J., Palenchar, P. M., Barnhart, L. E., and Paulson, J. L. (1998) Identification of a gene involved in the generation of 4-thiouridine in tRNA Nucleic Acids Res. 26, 2606-2610