Structural Basis of the Initial Binding of tRNAIle Lysidine Synthetase TilS with ATP and L-Lysine

Structure

Volumn 15, Issue 12, 2007, Pages 1642-1653

  Kuratani, Mitsuo ^a,b   Yoshikawa, Yuka ^c   Bessho, Yoshitaka ^b   Higashijima, Kyoko ^b   Ishii, Takeshi ^b   Shibata, Rie ^b   Takahashi, Seizo ^c   Yutani, Katsuhide ^d   Yokoyama, Shigeyuki ^a,b,d  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c JAPAN WOMEN'S UNIVERSITY   (Japan)

^d RIKEN HARIMA INSTITUTE   (Japan)

Author keywords

RNA

Indexed keywords

ADENOSINE TRIPHOSPHATE; ASPARTIC ACID; BACTERIAL ENZYME; CYTIDINE; INORGANIC PYROPHOSPHATASE; LYSIDINE SYNTHETHASE; LYSINE; MAGNESIUM ION; TRANSFER RNA; UNCLASSIFIED DRUG;

AQUIFEX AEOLICUS; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; AMINO ACYL-TRNA SYNTHETASES; LYSINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID;

AQUIFEX AEOLICUS; BACTERIA (MICROORGANISMS);

EID: 36749048020     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.09.020     Document Type: Article

References (49)

1. Adams P.D., Pannu N.S., Read R.J., and Brunger A.T. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl. Acad. Sci. USA 94 (1997) 5018-5023
2. Agris P.F., Vendeix F.A., and Graham W.D. tRNA's wobble decoding of the genome: 40 years of modification. J. Mol. Biol. 366 (2007) 1-13
3. Beeby M., O'Connor B.D., Ryttersgaard C., Boutz D.R., Perry L.J., and Yeates T.O. The genomics of disulfide bonding and protein stabilization in thermophiles. PLoS Biol. 3 (2005) e309
4. Bjork G., and Hagervall T.G. Transfer RNA modification. In: Curtiss III R., Bock A., Ingrahan J.L., Kaper J.B., Maloy S., Neidhardt F.C., Riley M.M., Squires C.L., and Wanner B.L. (Eds). Escherichia coli and Salmonella: Cellular and Molecular Biology (2005), ASM Press, Washington, DC. http://www.ecosal.org/ )
5. Bork P., and Koonin E.V. A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity. Proteins 20 (1994) 347-355
6. Crick F.H. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19 (1966) 548-555
7. Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L., Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392 (1998) 353-358
8. DeDecker B.S., O'Brien R., Fleming P.J., Geiger J.H., Jackson S.P., and Sigler P.B. The crystal structure of a hyperthermophilic archaeal TATA-box binding protein. J. Mol. Biol. 264 (1996) 1072-1084
9. Desogus G., Todone F., Brick P., and Onesti S. Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction. Biochemistry 39 (2000) 8418-8425
10. Gerber A.P., and Keller W. An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 286 (1999) 1146-1149
11. Goto M., Nakajima Y., and Hirotsu K. Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action. J. Biol. Chem. 277 (2002) 15890-15896
12. Goto M., Omi R., Miyahara I., Sugahara M., and Hirotsu K. Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction. J. Biol. Chem. 278 (2003) 22964-22971
13. Gouet P., Courcelle E., Stuart D.I., and Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308
14. Gouet P., Robert X., and Courcelle E. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31 (2003) 3320-3323
15. Harding M.M. Geometry of metal-ligand interactions in proteins. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 401-411
16. Ibba M., Francklyn C., and Cusack S. The Aminoacyl-tRNA Synthetases (2005), Landes Bioscience, Austin, TX
17. Ikeuchi Y., Soma A., Ote T., Kato J., Sekine Y., and Suzuki T. Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell 19 (2005) 235-246
18. Ishitani R., Nureki O., Nameki N., Okada N., Nishimura S., and Yokoyama S. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell 113 (2003) 383-394
19. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
20. Karlstrom M., Stokke R., Steen I.H., Birkeland N.K., and Ladenstein R. Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability. J. Mol. Biol. 345 (2005) 559-577
21. Knowlton J.R., Bubunenko M., Andrykovitch M., Guo W., Routzahn K.M., Waugh D.S., Court D.L., and Ji X. A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants. Biochemistry 42 (2003) 2275-2281
22. Kuratani M., Ishii R., Bessho Y., Fukunaga R., Sengoku T., Shirouzu M., Sekine S., and Yokoyama S. Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. J. Biol. Chem. 280 (2005) 16002-16008
23. Laskowski R.A., MacArthur M.W., Moss A.L., and Thornton J.M. PROCHECK. J. Appl. Crystallogr. 26 (1993) 283-291
24. Lemke C.T., and Howell P.L. The 1.6 Å crystal structure of E. coli argininosuccinate synthetase suggests a conformational change during catalysis. Structure 9 (2001) 1153-1164
25. Lemke C.T., and Howell P.L. Substrate induced conformational changes in argininosuccinate synthetase. J. Biol. Chem. 277 (2002) 13074-13081
26. Mallick P., Boutz D.R., Eisenberg D., and Yeates T.O. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl. Acad. Sci. USA 99 (2002) 9679-9684
27. Marck C., and Grosjean H. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8 (2002) 1189-1232
28. Meyer J., Clay M.D., Johnson M.K., Stubna A., Munck E., Higgins C., and Wittung-Stafshede P. A hyperthermophilic plant-type [2Fe-2S] ferredoxin from Aquifex aeolicus is stabilized by a disulfide bond. Biochemistry 41 (2002) 3096-3108
29. Mougous J.D., Lee D.H., Hubbard S.C., Schelle M.W., Vocadlo D.J., Berger J.M., and Bertozzi C.R. Molecular basis for G protein control of the prokaryotic ATP sulfurylase. Mol. Cell 21 (2006) 109-122
30. Muramatsu T., Nishikawa K., Nemoto F., Kuchino Y., Nishimura S., Miyazawa T., and Yokoyama S. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature 336 (1988) 179-181
31. Muramatsu T., Yokoyama S., Horie N., Matsuda A., Ueda T., Yamaizumi Z., Kuchino Y., Nishimura S., and Miyazawa T. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J. Biol. Chem. 263 (1988) 9261-9267
32. Nakanishi K., Fukai S., Ikeuchi Y., Soma A., Sekine Y., Suzuki T., and Nureki O. Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc. Natl. Acad. Sci. USA 102 (2005) 7487-7492
33. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
34. Pedone E., D'Ambrosio K., De Simone G., Rossi M., Pedone C., and Bartolucci S. Insights on a new PDI-like family: structural and functional analysis of a protein disulfide oxidoreductase from the bacterium Aquifex aeolicus. J. Mol. Biol. 356 (2006) 155-164
35. Rizzi M., Bolognesi M., and Coda A. A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure. Structure 6 (1998) 1129-1140
36. Roovers M., Wouters J., Bujnicki J.M., Tricot C., Stalon V., Grosjean H., and Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 32 (2004) 465-476
37. Silva F.J., Belda E., and Talens S.E. Differential annotation of tRNA genes with anticodon CAT in bacterial genomes. Nucleic Acids Res. 34 (2006) 6015-6022
38. Soma A., Ikeuchi Y., Kanemasa S., Kobayashi K., Ogasawara N., Ote T., Kato J., Watanabe K., Sekine Y., and Suzuki T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell 12 (2003) 689-698
39. Steiner T., Kaiser J.T., Marinkovic S., Huber R., and Wahl M.C. Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities. EMBO J. 21 (2002) 4641-4653
40. Suno R., Niwa H., Tsuchiya D., Zhang X., Yoshida M., and Morikawa K. Structure of the whole cytosolic region of ATP-dependent protease FtsH. Mol. Cell 22 (2006) 575-585
41. Suzuki T. Biosynthesis and function of tRNA wobble modifications. In: Grosjean H. (Ed). Fine-Tuning of RNA Functions by Modification and Editing (2005), Springer, Heidelberg 23-60
42. Tesmer J.J., Klem T.J., Deras M.L., Davisson V.J., and Smith J.L. The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Nat. Struct. Biol. 3 (1996) 74-86
43. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
44. Toth E.A., Worby C., Dixon J.E., Goedken E.R., Marqusee S., and Yeates T.O. The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds. J. Mol. Biol. 301 (2000) 433-450
45. Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30 (1997) 1022-1025
46. Vieille C., and Zeikus G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev. 65 (2001) 1-43
47. Waterman D.G., Ortiz-Lombardia M., Fogg M.J., Koonin E.V., and Antson A.A. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. J. Mol. Biol. 356 (2006) 97-110
48. Wolf J., Gerber A.P., and Keller W. tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J. 21 (2002) 3841-3851
49. Yokoyama S., and Nishimura S. Modified nucleosides and codon recognition. In: Soll D., and RajBhandary U. (Eds). tRNA: Structure, Biosynthesis, and Function (1995), ASM Press, Washington, DC 207-224