Amino Acids

, Volume 32, Issue 4, pp 479–482 | Cite as

Crystallization and preliminary X-ray diffraction analysis of E. coli arginyl-tRNA synthetase in complex form with a tRNAArg

  • M. Zhou
  • A. Azzi
  • X. Xia
  • E.-D. Wang
  • S.-X. Lin


Amino acids are building blocks of proteins, while aminoacyl-tRNA synthetases (aaRSs) catalyze the first reaction in such building: the biosynthesis of proteins. The E. coli arginyl-tRNA synthetase (ArgRS) has been crystallized in complex form with tRNAArg (B. stearothermophilus), at pH 5.6 using ammonium sulfate as a precipitating agent. Two crystal forms have been identified based on unit cell dimension. The complete data sets from both crystal forms have been collected with a primitive hexagonal space group. A data set of Form II crystals at 3.2 Å and 94% completeness has been obtained, with unit cell parameters a = b = 98.0 Å, c = 463.2 Å, and α = β = 90°, γ = 120°, being different from a = b = 110.8 Å, c = 377.8 Å for form I. The structure determination will demonstrate the interaction of these two macromolecules to understand the special mechanism of ArgRS that requires the presence of tRNA for amino acid activation. Such complex structure also provides a wide opening for inhibitor search using bioinformatics.

Keywords: Amino acids – Arginyl-tRNA synthetase – tRNAArg – Protein-RNA complex – Macromolecular crystallization – Amino acid activation – Aminoacylation – Protein biosynthesis 


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  1. Bernier, S, Dubois, DY, Habegger-Polomat, C, Gagnon, LP, Lapointe, J, Chenevert, R 2005Glutamylsulfamoyladenosine and pyroglutamylsulfamoyladenosine are competitive inhibitors of E. coli glutamyl-tRNA synthetaseJ Enzym Inhib Med Chem206167CrossRefGoogle Scholar
  2. Cavarelli, J, Delagoutte, B, Eriani, G, Gangloff, J, Moras, D 1998Yeast arginyl-tRNA synthetase with L-ArgEMBO J1754385448PubMedCrossRefGoogle Scholar
  3. Chou, KC 1994A molecular piston mechanism of pumping protons by bacteriorhodopsinAmino Acids7117CrossRefGoogle Scholar
  4. Chou, K-C 2004Structural bioinformatics and its impact to biomedical scienceCurr Med Chem1121052134PubMedGoogle Scholar
  5. Chou, K-C 2005Insights for modeling in the 3D structure of DNA-CBF3b complexJ Proteome Res416571660PubMedCrossRefGoogle Scholar
  6. Delagoutte, B, Moras, D, Cavarelli, J 2000tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates bindingEMBO J1955995610PubMedCrossRefGoogle Scholar
  7. Eriani, G, Delarue, M, Poch, O, Gangloff, J, Moras, D 1990Partition of tRNA synthetase into two classes based on mutually exclusive sets of sequence motifNature347203206PubMedCrossRefGoogle Scholar
  8. Eriani G, Cavarelli J (2005) Arginyl-tRNA synthetases. In: Ibba M, Francklyn C, Cusack SL (eds) The aminoacyl-tRNA synthetases. Landes bioscience/, pp 3–11Google Scholar
  9. Fersht, A, Gangloff, J, Dirheimer, G 1978Reaction pathway and rate-determining step in the aminoacylation of tRNAArg catalyzed by arginyl-tRNA synthetase from yeastBiochemistry1737403746PubMedCrossRefGoogle Scholar
  10. Gerlo, E, Freist, W, Charlier, J 1982Arginyl-tRNA synthetases from Escherichia coli K12: Specificity with regard to ATP analogs and their magnesium complexesHoppe Seylers Z Physiol Chem363365373PubMedGoogle Scholar
  11. Hampton Research (1999) Crystallization research tools 9, p 4Google Scholar
  12. Ibba, M, Soll, D 2000Aminoacyl-tRNA synthesisAnnu Rev Biochem69617650PubMedCrossRefGoogle Scholar
  13. Jancarik, J, Kim, SH 1991Sparse matrix sampling a screening method for crystallization of proteinsJ Appl Cryst24409411CrossRefGoogle Scholar
  14. Li, J, Yao, Y-N, Liu, M-F, Wang, ED 2003Arginyl-tRNA synthetase with signature sequence KMSK from Bacillus stearothermophilus Biochem J376773779PubMedCrossRefGoogle Scholar
  15. Lin, S-X, Shi, JP, Cheng, XD, Wang, Y-L 1988aArginyl-tRNA synthetase from Escherichia coli, purification by affinity chromatogaphy, properties, and steady-state kineticsBiochemistry2763436348CrossRefGoogle Scholar
  16. Lin, S-X, Wang, Q, Wang, Y-L 1988bInteraction between Escherichia coli arginyl-tRNA synthetase and its substratesBiochemistry2763486353CrossRefGoogle Scholar
  17. Liu, W, Wang, E-D, Wang, Y-L 1999A novel system for hyper expression and rapid purification of arginyl-tRNA synthetase from Escherichia coli Acta Biochim Biophys Sinica31494498Google Scholar
  18. Otwinowski, Z, Minor, W 1997Processing of X-ray diffraction data collected in oscillation modeCarter, CW,JrSweet, RM eds. Macromolecular crystallography. Part A. Methods in enzymologyAcademic PressNew York307326CrossRefGoogle Scholar
  19. Ravel, J, Wang, SF, Shive, W 1964Separation and properties of the glutamyl- and glutaminyl-tRNA synthetases of E. coli W Fed Proc23381Google Scholar
  20. Ravel, J, Wang, S, Heinemeyer, C, Shive, W 1965Glutamyl and glutaminyl ribonucleic acid synthetases of Escherichia coli W J Biol Chem240432438PubMedGoogle Scholar
  21. Shimada, A, Nureki, S, Goto, M, Takahashi, S, Yokoyama, S 2001Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetaseProc Natl Acad Sci USA981353713542PubMedCrossRefGoogle Scholar
  22. Zhang, C-T, Chou, K-C 1994A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequencesJ Mol Biol23818PubMedCrossRefGoogle Scholar
  23. Zhou, M, Wang, E-D, Campbell, RL, Wang, Y-L, Lin, S-X 1997Crystallization and preliminary X-ray diffraction analysis of arginyl-tRNA synthetase from Escherichia coli Protein Sci626362638PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • M. Zhou
    • 1
  • A. Azzi
    • 1
  • X. Xia
    • 2
  • E.-D. Wang
    • 2
  • S.-X. Lin
    • 1
    • 3
  1. 1.Laboratory of Molecular EndocrinologyCHUL Research Center and Laval UniversityQuébecCanada
  2. 2.State Key Laboratory of Molecular BiologyShanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes of Biological Sciences (SIBS)ShanghaiChina
  3. 3.Laboratory for Exchange Visitors and Structural Biology Platform, SIBCB, SIBSShanghaiChina

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