Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase

Biochemistry

Volumn 44, Issue 47, 2005, Pages 15488-15494

  Phannachet, Kulwadee ^a   Elias, Youssef ^a   Huang, Raven H ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CATALYSIS; ESCHERICHIA COLI; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; RNA; SUBSTRATES;

ASPARTIC ACID; PSEUDOURIDINE SYNTHASES; RNA SUBSTRATES; TYROSINE;

ENZYMES;

5 FLUORO 6 HYDROXYPSEUDOURIDINE; AMINO ACID DERIVATIVE; ARGININE; ASPARTIC ACID; HYDROXYL GROUP; LYSINE; PHENYL GROUP; PROTEIN RLUA; PROTEIN RSUA; PROTEIN TRUA; PROTEIN TRUB; PSEUDOURIDINE; PSEUDOURIDINE 55 SYNTHASE; SYNTHETASE; TRITIUM; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; GENE MUTATION; GENETIC CONSERVATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROPHOBICITY; MOLECULAR RECOGNITION; MUTANT; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN MOTIF; RNA BINDING; THERMOTOGA MARITIMA; WILD TYPE;

BINDING SITES; CATALYSIS; CATALYTIC DOMAIN; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; INTRAMOLECULAR LYASES; MUTATION, MISSENSE; RNA; SUBSTRATE SPECIFICITY; THERMOTOGA MARITIMA; TYROSINE;

ESCHERICHIA COLI; THERMOTOGA MARITIMA;

EID: 28244473650     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050961w     Document Type: Article

References (28)

1. Cohn, W. E., and Volkin, E. (1951) Nucleoside-5′-phosphates from ribonucleic acid, Nature 167, 483-484.
2. Yu, C. T., and Allen, F. W. (1959) Studies on an isomer of uridine isolated from ribonucleic acids, Biochim. Biophys. Acta 32, 393-406.
3. Scannell, J. P., Crestfield, A. M., and Allen, F. W. (1959) Methylation studies on various uracil derivatives and on an isomer of uridine isolated from ribonucleic acids. Biochim. Biophys. Acta 52, 406-412.
4. Cohn, W. E. (1959) 5-Ribosyl uracil, a carbon-carbon ribofuranosyl nucleoside in ribonucleic acids. Biochim. Biophys. Acta 32, 569-571.
5. Kammen, H. O., Marvel, C. C., Hardy. L., and Penhoet, E. E. (1988) Purification, structure, and properties of Escherichia coll tRNA pseudouridine synthase I, J. Biol. Chem. 263, 2255-2263.
6. Nurse, K., Wrzesinski, J., Bakin, A., Lane, B. G., and Ofengand, J. (1995) Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli, RNA 1, 102-112.
7. Wrzesinski, J., Bakin, A., Nurse, K., Lane. B. G., and Ofengand, J. (1995) Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 34, 8904-8913.
8. Wrzesinski, J., Nurse, K., Bakin, A., Lane, B. G., and Ofengand, J. (1995) A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe). RNA 1, 437-448.
9. Kaya, Y., and Ofengand, J. (2003) A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 9, 711-721.
10. Koonin. E. V. (1996) Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases, Nucleic Acids Res. 24, 2411-2415.
11. 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.
12. 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. U.S.A. 96, 14270-14275.
13. Foster, P. G., Huang, L., Santi, D. V., and Stroud, R. M. (2000) The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I, Nat. Struct. Biol. 7, 23-27.
14. 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.
15. Sivaraman, J., Sauve, V., Larocque, R., Stura, E. A., Schrag, J. D., Cygler, M., and Matte, A. (2002) Structure of the L6S rRNA pseudouridine synthase RsuA bound to uracil and UMP, Nat. Struct. Biol. 9, 353-358.
16. Sivaraman, J., Iannuzzi, P., Cygler, M., and Matte, A. (2004) Crystal structure of the R1uD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. J, Mol. Biol. 335, 87-101.
17. 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. U.S.A. 100, 12648-12653.
18. Phannachet, K., and Huang, R. H. (2004) Conformational change of pseudouridine 55 synthase upon its association with RNA substrate, Nucleic Acids Res. 32, 1422-1429.
19. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, in Methods in Enzymology, pp 307-326, Academic Press, San Diego, CA.
20. Navaza, J. (1994) AMoRe: an automated package for molecular replacement, Acta Crystallogr. A50, 157-163.
21. 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. A47, 110-119.
22. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D54, 905-921.
23. Gu, X., Yu, M., Ivanetich, K. M., and Sand, D. V. (1998) Molecular recognition of tRNA by tRNA pseudouridine 55 synthase, Biochemistry 37, 339-343.
24. Spedaliere, C. J., and Mueller, E. G. (2004) Not all pseudouridine synthases are potently inhibited by RNA containing 5-fluorouridine, RNA 10, 192-199.
25. 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.
26. Hoang, C., and Ferre-D'Amare, A. R. (2004) Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold, RNA 10, 1026-1033.
27. Kaya, Y., Del Campo. M., Ofengand, J., and Malhotra, A. (2004) Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold, J. Biol. Chem. 279, 18107-18110.
28. Ericsson, U. B., Nordlund, P., and Hallberg, B. M. (2004) X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold, FEBS Lett. 565, 59-64.