Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase

Journal of Molecular Biology

Volumn 378, Issue 3, 2008, Pages 634-652

  Yanagisawa, Tatsuo ^a   Ishii, Ryohei ^a,b   Fukunaga, Ryuya ^a,b   Kobayashi, Takatsugu ^a,b   Sakamoto, Kensaku ^a,b   Yokoyama, Shigeyuki ^a,b  

^a Yokohama Institute   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

aminoacyl tRNA synthetase; conformational changes; pyrrolysine; pyrrolysyl tRNA synthetase; tRNA

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; PYRROLYSYL TRNA SYNTHETASE; UNCLASSIFIED DRUG;

ACYLATION; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME STRUCTURE; METHANOSARCINA; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS; X RAY CRYSTALLOGRAPHY;

METHANOSARCINA MAZEI;

EID: 42249114824     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.02.045     Document Type: Article

References (56)

1. Ibba M., and Söll D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650
2. Eriani G., Delarue M., Poch O., Gangloff J., and Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 247 (1990) 203-206
3. Cusack S., Berthet-Colominas C., Hartlein M., Nassar N., and Leberman R. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 Å. Nature 347 (1990) 249-255
4. Asp. Science 252 (1991) 1682-1689
5. Cusack S. Eleven down and nine to go. Nat. Struct. Biol. 2 (1995) 824-831
6. Atkins J.F., and Gesteland R. Biochemistry, the 22nd amino acid. Science 296 (2002) 1409-1410
7. Ibba M., and Söll D. Genetic code: introducing pyrrolysine. Curr. Biol. 12 (2002) R464-R466
8. Gladyshev V.N., Jeang K.T., and Stadtman T.C. Selenocysteine, identified as the penultimate C-terminal residue in human T-cell thioredoxin reductase, corresponds to TGA in the human placental gene. Proc. Natl Acad. Sci. USA 93 (1996) 6146-6151
9. Commans S., and Böck A. Selenocysteine inserting tRNAs: an overview. FEMS Microbiol. Rev. 23 (1999) 335-351
10. Srinivasan G., James C.M., and Krzycki J.A. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296 (2002) 1459-1462
11. Hao B., Gong W., Ferguson T.K., James C.M., Krzycki J.A., and Chan M.K. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296 (2002) 1462-1466
12. CUA with pyrrolysine in vitro and in vivo. Nature 431 (2004) 333-335
13. Polycarpo C., Ambrogelly A., Berube A., Winbush S.M., McCloskey J.A., Crain P.F., et al. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc. Natl Acad. Sci. USA 101 (2004) 12450-12454
14. Yanagisawa T., Ishii R., Fukunaga R., Nureki O., and Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei. Acta Crystallogr. F 62 (2006) 1031-1033
15. Kavran J.M., Gundllapalli S., O'Donoghue P., Englert M., Söll D., and Steitz T.A. Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc. Natl Acad. Sci. USA 104 (2007) 11268-11273
16. Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A., et al. The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J. 13 (1994) 327-337
17. Belrhali H., Yaremchuk A., Tukalo M., Larsen K., Berthet-Colominas C., Leberman R., et al. Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Science 263 (1994) 1432-1436
18. Poterszman A., Delarue M., Thierry J.C., and Moras D. Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase. J. Mol. Biol. 244 (1994) 158-167
19. Belrhali H., Yaremchuk A., Tukalo M., Berthet-Colominas C., Rasmussen B., Bosecke P., et al. The structural basis for seryl-adenylate and Ap4A synthesis by seryl-tRNA synthetase. Structure 3 (1995) 341-352
20. Arnez J.G., Harris D.C., Mitschler A., Rees B., Francklyn C.S., and Moras D. Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate. EMBO J. 17 (1995) 4143-4155
21. Ser and a seryl-adenylate analogue reveals a conformational switch in the active site. EMBO J. 15 (1996) 2834-2842
22. Lys transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J. 15 (1996) 6321-6334
23. Arnez J.G., Augustine J.G., Moras D., and Francklyn C.S. The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase. Proc. Natl Acad. Sci. USA 94 (1997) 7144-7149
24. Aberg A., Yaremchuk A., Tukalo M., Rasmussen B., and Cusack S. Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase. Biochemistry 17 (1997) 3084-3094
25. Schmitt E., Moulinier L., Fujiwara S., Imanaka T., Thierry J.C., and Moras D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 17 (1998) 5227-5237
26. Berthet-Colominas C., Seignovert L., Hartlein M., Grotli M., Cusack S., and Leberman R. The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. EMBO J. 17 (1998) 2947-2960
27. Arnez J.G., Dock-Bregeon A.C., and Moras D. Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine. J. Mol. Biol. 286 (1999) 1449-1459
28. Reshetnikova L., Moor N., Lavrik O., and Vassylyev D.G. Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue. J. Mol. Biol. 287 (1999) 555-568
29. Asp in Escherichia coli-a snapshot of the second step. EMBO J. 18 (1999) 6532-6541
30. Qiu X., Janson C.A., Blackburn M.N., Chhohan I.K., Hibbs M., and Abdel-Meguid S.S. Cooperative structural dynamics and a novel fidelity mechanism in Histidyl-tRNA synthetases. Biochemistry 38 (1999) 12296-12304
31. 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
32. Asp complex reveals a tRNA-dependent control mechanism. EMBO J. 20 (2001) 5290-5301
33. Yaremchuk A., Tukalo M., Grotli M., and Cusack S. A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase. J. Mol. Biol. 309 (2001) 989-1002
34. Fishman R., Ankilova V., Moor N., and Safro M. Structure at 2.6 Å resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese. Acta Crystallogr. D 57 (2001) 1534-1544
35. Torres-Larios A., Sankaranarayanan R., Rees B., Dock-Bregeon A.C., and Moras D. Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase. J. Mol. Biol. 331 (2003) 201-211
36. Bovee M.L., Pierce M.A., and Francklyn C.S. Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase. Biochemistry 42 (2003) 15102-15113
37. Bilokapic S., Maier T., Ahel D., Gruic-Sovulj I., Söll D., Weygand-Durasevic I., and Ban N. Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. EMBO J. 25 (2005) 2498-2509
38. Swairjo M.A., and Schimmel P.R. Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Proc. Natl Acad. Sci. USA 102 (2005) 988-993
39. Phe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end. Biochemistry 45 (2006) 10572-10583
40. Kamtekar S., Kennedy W.D., Wang J., Stathopoulos C., Söll D., and Steitz T.A. The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases. Proc. Natl Acad. Sci. USA 100 (2003) 1673-1678
41. Crepin T., Yaremchuk A., Tukalo M., and Cusack S. Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain. Structure 14 (2006) 1511-1525
42. Ambrogelly A., Gundllapalli S., Herring S., Polycarpo C., Frauer C., and Söll D. Pyrrolysine is not hardwired for cotranslational insertion at UAG codons. Proc. Natl Acad. Sci. USA 104 (2007) 3141-3146
43. Onesti S., Desogus G., Brevet A., Chen J., Plateau P., Blanquet S., and Brick P. Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding. Biochemistry 39 (2000) 12853-12861
44. Sankaranarayanan R., Dock-Bregeon A.C., Rees B., Bovee M., Caillet J., Romby P., et al. Nature Struct. Biol. 7 (2000) 461-465
45. Shi H., and Moore P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA 6 (2000) 1091-1105
46. Herring S., Ambrogelly A., Polycarpo C.R., and Söll D. Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase. Nucleic Acids Res. 35 (2007) 1270-1278
47. Herring S., Ambrogelly A., Gundllapalli S., O'Donoghue P., Polycarpo C.R., and Söll D. The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity. FEBS Lett. 581 (2007) 3197-3203
48. Hao B., Zhao G., Kang P.T., Soares J.A., Ferguson T.K., Gallucci J., et al. Reactivity and chemical synthesis of L-pyrrolysine- the 22(nd) genetically encoded amino acid. Chem. Biol. 11 (2004) 1317-1324
49. Weeks C.M., and Miller R. Optimizing Shake- and -Bake for proteins. Acta Crystallogr. D 55 (1999) 492-500
50. Terwilliger T.C. SOLVE and RESOLVE: automated structure solution and density modification. Methods Enzymol. 374 (2003) 22-37
51. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
52. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system: a new soft ware suite for macromolecular structure determination. Acta Crystallogr. D 54 (1998) 905-921
53. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50 (1994) 760-763
54. Krissinel E., and Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60 (2004) 2256-2268
55. Varshney U., Lee C.P., and RajBhandary U.L. Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J. Biol. Chem. 266 (1991) 24712-24718
56. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680