Crystal structure of the 2′-5′ RNA ligase from Thermus thermophilus HB8

Journal of Molecular Biology

Volumn 329, Issue 5, 2003, Pages 903-911

  Kato, Miyuki ^a   Shirouzu, Mikako ^a,b   Terada, Takaho ^a,b   Yamaguchi, Hiroto ^a   Murayama, Kazutaka ^a   Sakai, Hiroaki ^a   Kuramitsu, Seiki ^b,c   Yokoyama, Shigeyuki ^a,b,d  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b RIKEN HARIMA INSTITUTE   (Japan)

^c OSAKA UNIVERSITY   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

2 5 RNA ligase; CPDase; Crystal structure; Thermus thermophilus; tRNA splicing

Indexed keywords

PHOSPHODIESTERASE; RNA LIGASE;

ARABIDOPSIS; ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ELECTRICITY; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; THERMUS THERMOPHILUS;

ARABIDOPSIS THALIANA; ARCHAEA; BACTERIA (MICROORGANISMS); THERMUS THERMOPHILUS;

EID: 0038206596     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00448-0     Document Type: Article

References (46)

1. Greer C.L., Peebles C.L., Gegenheimer P., Abelson J. Mechanism of action of a yeast RNA ligase in tRNA splicing. Cell. 32:1983;537-546.
2. Peebles C.L., Ogden R.C., Knapp G., Abelson J. Splicing of yeast tRNA precursors: a two-stage reaction. Cell. 18:1979;27-35.
3. Knapp G., Ogden R.C., Peebles C.L., Abelson J. Splicing of yeast tRNA precursors: structure of the reaction intermediates. Cell. 18:1979;37-45.
4. Peebles C.L., Gegenheimer P., Abelson J. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell. 32:1983;525-536.
5. Phizicky E.M., Schwartz R.C., Abelson J. Saccharomyces cerevisiae tRNA ligase. Purification of the protein and isolation of the structural gene. J. Biol. Chem. 261:1986;2978-2986.
6. Westaway S.K., Phizicky E.M., Abelson J. Structure and function of the yeast tRNA ligase gene. J. Biol. Chem. 263:1988;3171-3176.
7. Xu Q., Teplow D., Lee T.D., Abelson J. Domain structure in yeast tRNA ligase. Biochemistry. 29:1990;6132-6138.
8. Westaway S.K., Belford H.G., Apostol B.L., Abelson J., Greer C.L. Novel activity of a yeast ligase deletion polypeptide. Evidence for GTP- dependent tRNA splicing. J. Biol. Chem. 268:1993;2435-2443.
9. Belford H.G., Westaway S.K., Abelson J., Greer C.L. Multiple nucleotide cofactor use by yeast ligase in tRNA splicing. Evidence for independent ATP- and GTP-binding sites. J. Biol. Chem. 268:1993;2444-2450.
10. McCraith S.M., Phizicky E.M. A highly specific phosphatase from Saccharomyces cerevisiae implicated in tRNA splicing. Mol. Cell. Biol. 10:1990;1049-1055.
11. McCraith S.M., Phizicky E.M. An enzyme from Saccharomyces cerevisiae uses NAD+ to transfer the splice junction 2′-phosphate from ligated tRNA to an acceptor molecule. J. Biol. Chem. 266:1991;11986-11992.
12. Culver G.M., McCraith S.M., Zillmann M., Kierzek R., Michaud N., LaReau R.D., Turner D.H., Phizicky E.M. An NAD derivative produced during transfer RNA splicing: ADP-ribose 1″-2″ cyclic phosphate. Science. 261:1993;206-208.
13. Greer C., Javor B., Abelson J. RNA ligase in bacteria: formation of a 2′,5′ linkage by an E. coli extract. Cell. 33:1983;899-906.
14. Arn E.A., Abelson J.N. The 2′-5′ RNA ligase of Escherichia coli: purification, cloning, and genomic disruption. J. Biol. Chem. 271:1996;31145-31153.
15. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
16. Hofmann A., Zdanov A., Genschik P., Ruvinov S., Filipowicz W., Wlodawer A. Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction. EMBO J. 19:2000;6207-6217.
17. Hofmann A., Grella M., Botos I., Filipowicz W., Wlodawer A. Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana. J. Biol. Chem. 277:2002;1419-1425.
18. Nasr F., Filipowicz W. Characterization of the Saccharomyces cerevisiae cyclic nucleotide phosphodiesterase involved in the metabolism of ADP-ribose 1″,2″-cyclic phosphate. Nucl. Acids Res. 28:2000;1676-1683.
19. Nakai T., Okada K., Akutsu S., Miyahara I., Kawaguchi S., Kato R., et al. Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate. Biochemistry. 38:1999;2413-2424.
20. Vieille C., Zeilus J.G. Thermozymes: identifying molecular determinants of protein structural and functional stability. Trends Biotechnol. 14:1996;183-190.
21. Kawamura S., Kakuta Y., Tanaka I., Hikichi K., Kuhara S., Yamasaki N., et al. Glycine-15 in the bend between two alpha-helices can explain the thermostability of DNA binding protein HU from Bacillus stearothermophilus. Biochemistry. 35:1996;1195-1200.
22. Matthews B.W., Nicholson H., Becktel W. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl Acad. Sci. USA. 84:1987;6663-6667.
23. Kimura S., Kanaya S., Nakamura H. Thermostabilization of Escherichia coli ribonuclease HI by replacing left-handed helical Lys95 with Gly or Asn. J. Biol. Chem. 267:1992;22014-22017.
24. Nureki O., Shirouzu M., Hashimoto K., Ishitani R., Terada T., Tamakoshi M., et al. An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallog. sect. D. 58:2002;1129-1137.
25. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
26. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallog. sect. D. 55:1999;849-861.
27. Terwilliger T.C. Maximum likelihood density modification. Acta Crystallog. sect. D. 56:2000;965-972.
28. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
29. Brünger A.T., Adams P.D., Clore G.M., Delano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921.
30. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
31. Merritt E.A., Bacon D.J. Raster3D photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
32. Nicholls A., Sharp K.A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;281-296.
33. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
34. Abelson J., Trotta C.R., Li H. tRNA splicing. J. Biol. Chem. 273:1998;12685-12688.
35. White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D., Dodson R.J., et al. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. 286:1999;1571-1577.
36. Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H., et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329.
37. Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., et al. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature. 390:1997;237-238.
38. Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S., et al. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7:2000;331-338.
39. Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L., Graham D.E., et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 392:1998;353-358.
40. Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., et al. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5:1998;55-76.
41. Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H., Dubois J., Aldredge T., et al. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J. Bacteriol. 179:1997;7135-7155.
42. Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 273:1996;1058-1073.
43. Klenk H.P., Clayton R.A., Tomb J.F., White O., Nelson K.E., Ketchum K.A., et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 390:1998;364-370.
44. Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K., et al. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 6:1999;83-101.
45. Genschik P., Hall J., Filipowicz W. Cloning and characterization of the Arabidopsis cyclic phosphodiesterase which hydrolyzes ADP-ribose 1″,2″-cyclic phosphate and nucleoside 2′,3′-cyclic phosphates. J. Biol. Chem. 272:1997;13211-13219.
46. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25:1997;4876-4882.