3nem › Citations

Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.

Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D
EMBO J 17 5227-37 (1998)
Related entries: 1b8a, 3nel, 3nen

Cited: 75 times
EuropePMC logo PMID: 9724658

Abstract

The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 A resolution. The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs. In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNAAsp and tRNAAsn. Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes.

Articles - 3nem mentioned but not cited (5)

  1. Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major. Gowri VS, Ghosh I, Sharma A, Madhubala R. BMC Genomics 13 621 (2012)
  2. Structural basis for microcin C7 inactivation by the MccE acetyltransferase. Agarwal V, Metlitskaya A, Severinov K, Nair SK. J Biol Chem 286 21295-21303 (2011)
  3. Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Brylinski M. Front Genet 4 118 (2013)
  4. Distinct Conformation of ATP Molecule in Solution and on Protein. Kobayashi E, Yura K, Nagai Y. Biophysics (Nagoya-shi) 9 1-12 (2013)
  5. Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori. Songsiriritthigul C, Suebka S, Chen CJ, Fuengfuloy P, Chuawong P. Acta Crystallogr F Struct Biol Commun 73 62-69 (2017)


Reviews citing this publication (10)

  1. Aminoacyl-tRNA synthesis. Ibba M, Soll D. Annu Rev Biochem 69 617-650 (2000)
  2. Aminoacyl-tRNA synthetases: a new image for a classical family. Martinis SA, Plateau P, Cavarelli J, Florentz C. Biochimie 81 683-700 (1999)
  3. Archaeal aminoacyl-tRNA synthesis: diversity replaces dogma. Tumbula D, Vothknecht UC, Kim HS, Ibba M, Min B, Li T, Pelaschier J, Stathopoulos C, Becker H, Söll D. Genetics 152 1269-1276 (1999)
  4. Operational RNA code for amino acids in relation to genetic code in evolution. Ribas de Pouplana L, Schimmel P. J Biol Chem 276 6881-6884 (2001)
  5. Emergence and evolution. Bullwinkle TJ, Ibba M. Top Curr Chem 344 43-87 (2014)
  6. From protein sequence to function. Danchin A. Curr Opin Struct Biol 9 363-367 (1999)
  7. Histidyl-tRNA synthetase. Freist W, Verhey JF, Rühlmann A, Gauss DH, Arnez JG. Biol Chem 380 623-646 (1999)
  8. Molecular bases of thermophily in hyperthermophiles. Imanaka T. Proc Jpn Acad Ser B Phys Biol Sci 87 587-602 (2011)
  9. Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea. Imanaka T, Atomi H. Chem Rec 2 149-163 (2002)
  10. An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research. Rashid N, Aslam M. Folia Microbiol (Praha) 65 67-78 (2020)

Articles citing this publication (60)

  1. Dissecting subunit interfaces in homodimeric proteins. Bahadur RP, Chakrabarti P, Rodier F, Janin J. Proteins 53 708-719 (2003)
  2. Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. Martin G, Keller W, Doublié S. EMBO J 19 4193-4203 (2000)
  3. Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Curnow AW, Tumbula DL, Pelaschier JT, Min B, Söll D. Proc Natl Acad Sci U S A 95 12838-12843 (1998)
  4. Plant perception of β-aminobutyric acid is mediated by an aspartyl-tRNA synthetase. Luna E, van Hulten M, Zhang Y, Berkowitz O, López A, Pétriacq P, Sellwood MA, Chen B, Burrell M, van de Meene A, Pieterse CM, Flors V, Ton J. Nat Chem Biol 10 450-456 (2014)
  5. Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. J Mol Biol 378 634-652 (2008)
  6. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Min B, Pelaschier JT, Graham DE, Tumbula-Hansen D, Söll D. Proc Natl Acad Sci U S A 99 2678-2683 (2002)
  7. Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis. Mao L, Wang Y, Liu Y, Hu X. J Mol Biol 336 787-807 (2004)
  8. A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase. Yaremchuk A, Tukalo M, Grøtli M, Cusack S. J Mol Biol 309 989-1002 (2001)
  9. Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. Retailleau P, Huang X, Yin Y, Hu M, Weinreb V, Vachette P, Vonrhein C, Bricogne G, Roversi P, Ilyin V, Carter CW. J Mol Biol 325 39-63 (2003)
  10. The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism. Moulinier L, Eiler S, Eriani G, Gangloff J, Thierry JC, Gabriel K, McClain WH, Moras D. EMBO J 20 5290-5301 (2001)
  11. When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism. Roy H, Becker HD, Reinbolt J, Kern D. Proc Natl Acad Sci U S A 100 9837-9842 (2003)
  12. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. Archontis G, Simonson T, Karplus M. J Mol Biol 306 307-327 (2001)
  13. When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Denessiouk KA, Johnson MS. Proteins 38 310-326 (2000)
  14. Conformational diversity of ligands bound to proteins. Stockwell GR, Thornton JM. J Mol Biol 356 928-944 (2006)
  15. Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue. Reshetnikova L, Moor N, Lavrik O, Vassylyev DG. J Mol Biol 287 555-568 (1999)
  16. A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity. Nakatani M, Ezaki S, Atomi H, Imanaka T. J Bacteriol 182 6424-6433 (2000)
  17. Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine. Arnez JG, Dock-Bregeon AC, Moras D. J Mol Biol 286 1449-1459 (1999)
  18. On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM. Proteins 78 1120-1136 (2010)
  19. Control of catalytic cycle by a pair of analogous tRNA modification enzymes. Christian T, Lahoud G, Liu C, Hou YM. J Mol Biol 400 204-217 (2010)
  20. The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain. Sauter C, Lorber B, Cavarelli J, Moras D, Giegé R. J Mol Biol 299 1313-1324 (2000)
  21. On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Mulkidjanian AY, Galperin MY. Biol Direct 4 27 (2009)
  22. Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase. Torres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D. J Mol Biol 331 201-211 (2003)
  23. BOF: a novel family of bacterial OB-fold proteins. Ginalski K, Kinch L, Rychlewski L, Grishin NV. FEBS Lett 567 297-301 (2004)
  24. Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. Charron C, Roy H, Blaise M, Giegé R, Kern D. EMBO J 22 1632-1643 (2003)
  25. An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase. Briand C, Poterszman A, Eiler S, Webster G, Thierry J, Moras D. J Mol Biol 299 1051-1060 (2000)
  26. Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation. Blaise M, Bailly M, Frechin M, Behrens MA, Fischer F, Oliveira CL, Becker HD, Pedersen JS, Thirup S, Kern D. EMBO J 29 3118-3129 (2010)
  27. Pleiotropic effects of ATP.Mg2+ binding in the catalytic cycle of ubiquitin-activating enzyme. Tokgöz Z, Bohnsack RN, Haas AL. J Biol Chem 281 14729-14737 (2006)
  28. Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates. Rees B, Webster G, Delarue M, Boeglin M, Moras D. J Mol Biol 299 1157-1164 (2000)
  29. Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. Francis BR. J Mol Evol 77 134-158 (2013)
  30. Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms. Tumbula-Hansen D, Feng L, Toogood H, Stetter KO, Söll D. J Biol Chem 277 37184-37190 (2002)
  31. Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase. Thompson D, Plateau P, Simonson T. Chembiochem 7 337-344 (2006)
  32. Thermodynamic properties distinguish human mitochondrial aspartyl-tRNA synthetase from bacterial homolog with same 3D architecture. Neuenfeldt A, Lorber B, Ennifar E, Gaudry A, Sauter C, Sissler M, Florentz C. Nucleic Acids Res 41 2698-2708 (2013)
  33. Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase. Iwasaki W, Sekine S, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S. J Mol Biol 360 329-342 (2006)
  34. Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Feng L, Tumbula-Hansen D, Toogood H, Soll D. Proc Natl Acad Sci U S A 100 5676-5681 (2003)
  35. Peculiar inhibition of human mitochondrial aspartyl-tRNA synthetase by adenylate analogs. Messmer M, Blais SP, Balg C, Chênevert R, Grenier L, Lagüe P, Sauter C, Sissler M, Giegé R, Lapointe J, Florentz C. Biochimie 91 596-603 (2009)
  36. Structural basis of tRNA agmatinylation essential for AUA codon decoding. Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T. Nat Struct Mol Biol 18 1275-1280 (2011)
  37. A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site. Yanagisawa T, Sumida T, Ishii R, Yokoyama S. Acta Crystallogr D Biol Crystallogr 69 5-15 (2013)
  38. Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases. Kaiser F, Bittrich S, Salentin S, Leberecht C, Haupt VJ, Krautwurst S, Schroeder M, Labudde D. PLoS Comput Biol 14 e1006101 (2018)
  39. Crystal structure of the aspartyl-tRNA synthetase from Entamoeba histolytica. Merritt EA, Arakaki TL, Larson ET, Kelley A, Mueller N, Napuli AJ, Zhang L, Deditta G, Luft J, Verlinde CL, Fan E, Zucker F, Buckner FS, Van Voorhis WC, Hol WG. Mol Biochem Parasitol 169 95-100 (2010)
  40. Molecular modeling of purinergic receptor P2Y12 and interaction with its antagonists. Zhan C, Yang J, Dong XC, Wang YL. J Mol Graph Model 26 20-31 (2007)
  41. Sequence, structure and evolutionary analysis of cold shock domain proteins, a member of OB fold family. Amir M, Kumar V, Dohare R, Islam A, Ahmad F, Hassan MI. J Evol Biol 31 1903-1917 (2018)
  42. Structural flexibility of the methanogenic-type seryl-tRNA synthetase active site and its implication for specific substrate recognition. Bilokapic S, Rokov Plavec J, Ban N, Weygand-Durasevic I. FEBS J 275 2831-2844 (2008)
  43. Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases. Liu C, Sanders JM, Pascal JM, Hou YM. RNA 18 213-221 (2012)
  44. Crystal structure of the archaeal asparagine synthetase: interrelation with aspartyl-tRNA and asparaginyl-tRNA synthetases. Blaise M, Fréchin M, Oliéric V, Charron C, Sauter C, Lorber B, Roy H, Kern D. J Mol Biol 412 437-452 (2011)
  45. Sequence-structure mapping errors in the PDB: OB-fold domains. Venclovas C, Ginalski K, Kang C. Protein Sci 13 1594-1602 (2004)
  46. Structural asymmetry of the terminal catalytic complex in selenocysteine synthesis. French RL, Gupta N, Copeland PR, Simonović M. J Biol Chem 289 28783-28794 (2014)
  47. Taxonomic distribution, repeats, and functions of the S1 domain-containing proteins as members of the OB-fold family. Deryusheva EI, Machulin AV, Selivanova OM, Galzitskaya OV. Proteins 85 602-613 (2017)
  48. Asymmetric behavior of archaeal prolyl-tRNA synthetase. Ambrogelly A, Kamtekar S, Stathopoulos C, Kennedy D, Söll D. FEBS Lett 579 6017-6022 (2005)
  49. Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations. Thompson D, Lazennec C, Plateau P, Simonson T. Proteins 71 1450-1460 (2008)
  50. Mapping hidden potential identity elements by computing the average discriminating power of individual tRNA positions. Szenes A, Pál G. DNA Res 19 245-258 (2012)
  51. Molecular dynamics simulations of LysRS: an asymmetric state. Hughes SJ, Tanner JA, Miller AD, Gould IR. Proteins 62 649-662 (2006)
  52. An idiosyncratic serine ordering loop in methanogen seryl-tRNA synthetases guides substrates through seryl-tRNASer formation. Dulic M, Pozar J, Bilokapic S, Weygand-Durasevic I, Gruic-Sovulj I. Biochimie 93 1761-1769 (2011)
  53. A single amino acid substitution affects the substrate specificity of the seryl-tRNA synthetase homologue. Maršavelski A, Lesjak S, Močibob M, Weygand-Đurašević I, Tomić S. Mol Biosyst 10 3207-3216 (2014)
  54. Lysyl-tRNA synthetase from Bacillus stearothermophilus: the Trp314 residue is shielded in a non-polar environment and is responsible for the fluorescence changes observed in the amino acid activation reaction. Takita T, Nakagoshi M, Inouye K, Tonomura B. J Mol Biol 325 677-695 (2003)
  55. Aminoacylation at the Atomic Level in Class IIa Aminoacyl-tRNA Synthetases. Arnez JG, Sankaranarayanan R, Dock-Bregeon AC, Francklyn CS, Moras D. J Biomol Struct Dyn 17 Suppl 1 23-27 (2000)
  56. Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote. Furukawa R, Yokobori SI, Sato R, Kumagawa T, Nakagawa M, Katoh K, Yamagishi A. J Mol Evol 90 73-94 (2022)
  57. An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening. Xiang M, Xia K, Chen B, Luo Z, Yu Y, Jiang L, Zhou H. Nucleic Acids Res 51 4637-4649 (2023)
  58. Crystallization and preliminary X-ray crystallographic study of a putative aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7. Suzuki K, Sato Y, Maeda Y, Shimizu S, Hossain MT, Ubukata S, Sekiguchi T, Takénaka A. Acta Crystallogr Sect F Struct Biol Cryst Commun 63 608-612 (2007)
  59. Overproduction of the N-terminal anticodon-binding domain of the non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori for crystallization and NMR measurements. Fuengfuloy P, Chuawong P, Suebka S, Wattana-Amorn P, Williams C, Crump MP, Songsiriritthigul C. Protein Expr Purif 89 25-32 (2013)
  60. Sequential magnesium binding facilitates lysyl-tRNA synthetase to recognize ATP. Hei Z, Fang P. Biochem Biophys Rep 33 101426 (2023)


Quick links