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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 1632-43 (2003)
Cited: 30 times
EuropePMC logo PMID: 12660169

Abstract

In most organisms, tRNA aminoacylation is ensured by 20 aminoacyl-tRNA synthetases (aaRSs). In eubacteria, however, synthetases can be duplicated as in Thermus thermophilus, which contains two distinct AspRSs. While AspRS-1 is specific, AspRS-2 is non-discriminating and aspartylates tRNA(Asp) and tRNA(Asn). The structure at 2.3 A resolution of AspRS-2, the first of a non-discriminating synthetase, was solved. It differs from that of AspRS-1 but has resemblance to that of discriminating and archaeal AspRS from Pyrococcus kodakaraensis. The protein presents non-conventional features in its OB-fold anticodon-binding domain, namely the absence of a helix inserted between two beta-strands of this fold and a peculiar L1 loop differing from the large loops known to interact with tRNA(Asp) identity determinant C36 in conventional AspRSs. In AspRS-2, this loop is small and structurally homologous to that in AsnRSs, including conservation of a proline. In discriminating Pyrococcus AspRS, the L1 loop, although small, lacks this proline and is not superimposable with that of AspRS-2 or AsnRS. Its particular status is demonstrated by a loop-exchange experiment that renders the Pyrococcus AspRS non-discriminating.

Articles - 1n9w mentioned but not cited (5)

  1. 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)
  2. Evaluating the solution from MrBUMP and BALBES. Keegan RM, Long F, Fazio VJ, Winn MD, Murshudov GN, Vagin AA. Acta Crystallogr D Biol Crystallogr 67 313-323 (2011)
  3. 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)
  4. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Mukai T, Amikura K, Fu X, Söll D, Crnković A. Front Genet 12 794509 (2021)
  5. Isolation, crystallization and preliminary X-ray analysis of the transamidosome, a ribonucleoprotein involved in asparagine formation. Bailly M, Blaise M, Lorber B, Thirup S, Kern D. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 577-581 (2009)


Reviews citing this publication (4)

  1. On the evolution of structure in aminoacyl-tRNA synthetases. O'Donoghue P, Luthey-Schulten Z. Microbiol Mol Biol Rev 67 550-573 (2003)
  2. Transfer RNA travels from the cytoplasm to organelles. Rubio MA, Hopper AK. Wiley Interdiscip Rev RNA 2 802-817 (2011)
  3. Transfer RNA: a dancer between charging and mis-charging for protein biosynthesis. Zhou X, Wang E. Sci China Life Sci 56 921-932 (2013)
  4. Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites. Nasim F, Qureshi IA. ACS Omega 8 14884-14899 (2023)

Articles citing this publication (21)

  1. Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Rinehart J, Krett B, Rubio MA, Alfonzo JD, Söll D. Genes Dev 19 583-592 (2005)
  2. Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53. Liao JC, Lam R, Brazda V, Duan S, Ravichandran M, Ma J, Xiao T, Tempel W, Zuo X, Wang YX, Chirgadze NY, Arrowsmith CH. Structure 19 418-429 (2011)
  3. The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis. Bailly M, Blaise M, Lorber B, Becker HD, Kern D. Mol Cell 28 228-239 (2007)
  4. Crystal structure of a non-discriminating glutamyl-tRNA synthetase. Schulze JO, Masoumi A, Nickel D, Jahn M, Jahn D, Schubert WD, Heinz DW. J Mol Biol 361 888-897 (2006)
  5. 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)
  6. 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)
  7. Small but powerful, the primary endosymbiont of moss bugs, Candidatus Evansia muelleri, holds a reduced genome with large biosynthetic capabilities. Santos-Garcia D, Latorre A, Moya A, Gibbs G, Hartung V, Dettner K, Kuechler SM, Silva FJ. Genome Biol Evol 6 1875-1893 (2014)
  8. Novel tRNA aminoacylation mechanisms. Cathopoulis T, Chuawong P, Hendrickson TL. Mol Biosyst 3 408-418 (2007)
  9. The nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori: anticodon-binding domain mutations that impact tRNA specificity and heterologous toxicity. Chuawong P, Hendrickson TL. Biochemistry 45 8079-8087 (2006)
  10. tRNA-dependent asparagine formation in prokaryotes: characterization, isolation and structural and functional analysis of a ribonucleoprotein particle generating Asn-tRNA(Asn). Bailly M, Blaise M, Roy H, Deniziak M, Lorber B, Birck C, Becker HD, Kern D. Methods 44 146-163 (2008)
  11. Evolution of the genetic triplet code via two types of doublet codons. Wu HL, Bagby S, van den Elsen JM. J Mol Evol 61 54-64 (2005)
  12. 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)
  13. Divergent anticodon recognition in contrasting glutamyl-tRNA synthetases. Lee J, Hendrickson TL. J Mol Biol 344 1167-1174 (2004)
  14. Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. O'Donoghue P, Sheppard K, Nureki O, Söll D. Proc Natl Acad Sci U S A 108 20485-20490 (2011)
  15. Conserved discrimination against misacylated tRNAs by two mesophilic elongation factor Tu orthologs. Cathopoulis TJ, Chuawong P, Hendrickson TL. Biochemistry 47 7610-7616 (2008)
  16. Novel and unique domains in aminoacyl-tRNA synthetases from human fungal pathogens Aspergillus niger, Candida albicans and Cryptococcus neoformans. Datt M, Sharma A. BMC Genomics 15 1069 (2014)
  17. Recognition of tRNAGln by Helicobacter pylori GluRS2--a tRNAGln-specific glutamyl-tRNA synthetase. Chang KM, Hendrickson TL. Nucleic Acids Res 37 6942-6949 (2009)
  18. Two residues in the anticodon recognition domain of the aspartyl-tRNA synthetase from Pseudomonas aeruginosa are individually implicated in the recognition of tRNAAsn. Bernard D, Akochy PM, Beaulieu D, Lapointe J, Roy PH. J Bacteriol 188 269-274 (2006)
  19. A water-mediated and substrate-assisted aminoacylation mechanism in the discriminating aminoacyl-tRNA synthetase GlnRS and non-discriminating GluRS. Aboelnga MM, Hayward JJ, Gauld JW. Phys Chem Chem Phys 19 25598-25609 (2017)
  20. 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)
  21. 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)


Related citations provided by authors (1)

  1. Crystallization and preliminary X-ray diffraction data of the second and archaebacterial-type aspartyl-tRNA synthetase from Thermus thermophilus. Charron C, Roy H, Lorber L, Kern D, Giege R Acta Crystallogr. D Biol. Crystallogr. 57 1177-1179 (2001)

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