Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold

RNA

Volumn 10, Issue 7, 2004, Pages 1026-1033

  Hoang, Charmaine ^a   Ferré D'Amaré, Adrian R ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Pus7p; RNA modification; SIRAS; TruD; X ray crystallography

Indexed keywords

PROTEIN PUS7P; PROTEIN TRUD; PSEUDOURIDINE SYNTHASE; RNA; SYNTHETASE; UNCLASSIFIED DRUG;

ARCHAEBACTERIUM; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; ESCHERICHIA COLI; EUKARYOTE; GENETIC CONSERVATION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING;

AMINO ACID SEQUENCE; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; INTRAMOLECULAR TRANSFERASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

ARCHAEA; ESCHERICHIA; ESCHERICHIA COLI; EUKARYOTA;

EID: 3042618760     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7240504     Document Type: Article

References (35)

1. Aravind, L. and Koonin, E.V. 1999. Novel predicted RNA-binding domains associated with the translation machinery. J. Mol. Evol. 48:291-302.
2. Behm-Ansmant, I., Urban, A., Ma, X., Yu, Y.T., Motorin, Y., and Branlant, C. 2003. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:ψ-synthase also acting on tRNAs. RNA 9: 1371-1382.
3. Brünger, A.T., Adams, P.D., Clore, G.M., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., et al. 1998. Crystallography and NMR system: A new software system for macromolecular structure determination. Acta Crystallogr. D 54: 905-921.
4. Carson, M. 1997. Ribbons. Meth. Enzymol. 277: 493-505.
5. Del Campo, M., Ofengand, J., and Malhotra, A. 2004. Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli. RNA 10:231-239.
6. Doublié, S. 1997. Preparation of selenomethionyl proteins for phase determination. Meth. Enzymol. 276: 523-530.
7. Ericsson, U.B., Andersson, M.E., Engvall, B., Nordlund, P., and Hallberg, B.M. 2004. Expression, purification, crystallization and preliminary diffraction studies of the tRNA pseudouridine synthase TruD from Escherichia coli. Acta Crystallogr. D 60: 775-776.
8. Ferré-D'Amaré, A.R. 2003. RNA-modifying enzymes. Curr. Opin. Struct. Biol. 13: 49-55.
9. Foster, P.G., Huang, L., Santi, D., and Stroud, R.M. 2000. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Nat. Struct. Biol. 7: 23-27.
10. Hoang, C. and Ferré-D'Amaré, A.R. 2001. Cocrystal structure of a tRNA ψ55 pseudouridine synthase: Nucleotide flipping by an RNA-modifying enzyme. Cell 71: 929-939.
11. Holm, L. and Sander, C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233: 123-138.
12. Jancarik, J. and Kim, S.-H. 1991. Sparse matrix sampling: A screening method for crystallization of proteins. J. Appl. Cryst. 24: 409-411.
13. 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: 110-119.
14. Jung, J. and Lee, B. 2001. Circularly permuted proteins in the protein structure database. Protein Sci. 10: 1881-1886.
15. Kaya, Y. and Ofengand, J. 2003. A novel unanticipated type of pseudourdine synthase with homologs in bacteria archaea and eukarya. RNA 9: 711-721.
16. 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.
17. 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.
18. Laskowski, R.J., Macarthur, M.W., Moss, D.S., and Thornton, J.M. 1993. PROCHECK: A program to check stereochemical quality of protein structures. J. Appl. Cryst. 26: 283-290.
19. Lemke, C.T., Smith, G.D., and Howell, P.L. 2002. S-SAD, Se-AD and S/Se-SIRAS using Cu Kα radiation: Why wait for synchrotron time? Acta Crystallogr. D 58: 2096-2101.
20. Lindqvist, Y. and Schneider, G. 1997. Circular permutations of natural protein sequences: Structural evidence. Curr. Opin. Struct. Biol. 7: 422-427.
21. Ma, X., Zhao, X., and Yu, Y.-T. 2003. Pseudouridylation of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J. 22: 1889-1897.
22. Mueller, E.G. 2002. Chips off the old block. Nat. Struct. Biol. 9: 320-322.
23. Newby, M.I. and Greenbaum, N.L. 2002. Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine. Nat. Struct. Biol. 9: 958-965.
24. Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol. 276: 307-326.
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. 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.
27. Sander, C. and Schneider, R. 1991. Database of homology-derived protein structures and structural meaning of sequence alignment. Proteins 9: 56-68.
28. Sivaraman, J., Sauve, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M., and Matte, A. 2002. Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nat. Struct. Biol. 9: 353-358.
29. Sivaraman, J., Iannuzzi, P., Cygler, M., and Matte, A. 2004. Crystal structure of the RluD 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.
30. Spedaliere, C.J. and Mueller, E.G. 2004. Not all pseudouridine synthases are potently inhibited by RNA containing 5-fluorouridine. RNA 10: 192-199.
31. Terwilliger, T.C. and Berendzen, J. 1999. Automated MAD and MIR structure solution. Acta Crystallogr. D 55: 849-861.
32. Todd, A.E., Orengo, C.A., and Thornton, J.M. 2002. Plasticity of enzyme active sites. Trends Biochem. Sci. 27: 419-426.
33. Uliel, S., Fliess, A., and Unger, R. 2001. Naturally occurring circular permutations in proteins. Protein Eng. 14: 533-542.
34. Yu, Y.-T., Shu, M.-D., and Steitz, J.A. 1998. Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing. EMBO J. 17: 5783-5795.
35. Zhao, X. and Yu, Y.-T. 2004. Pseudouridines in and near the branch site recognition region of U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing in Xenopus oocytes. RNA 10: 681-690.