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C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec).

Sherrer RL, Araiso Y, Aldag C, Ishitani R, Ho JM, Söll D, Nureki O
Nucleic Acids Res 39 1034-41 (2011)
Cited: 19 times
EuropePMC logo PMID: 20870747

Abstract

O-Phosphoseryl-tRNA kinase (PSTK) is the key enzyme in recruiting selenocysteine (Sec) to the genetic code of archaea and eukaryotes. The enzyme phosphorylates Ser-tRNA(Sec) to produce O-phosphoseryl-tRNA(Sec) (Sep-tRNA(Sec)) that is then converted to Sec-tRNA(Sec) by Sep-tRNA:Sec-tRNA synthase. Earlier we reported the structure of the Methanocaldococcus jannaschii PSTK (MjPSTK) complexed with AMPPNP. This study presents the crystal structure (at 2.4-Å resolution) of MjPSTK complexed with an anticodon-stem/loop truncated tRNA(Sec) (Mj*tRNA(Sec)), a good enzyme substrate. Mj*tRNA(Sec) is bound between the enzyme's C-terminal domain (CTD) and N-terminal kinase domain (NTD) that are connected by a flexible 11 amino acid linker. Upon Mj*tRNA(Sec) recognition the CTD undergoes a 62-Å movement to allow proper binding of the 7-bp D-stem. This large reorganization of the PSTK quaternary structure likely provides a means by which the unique tRNA(Sec) species can be accurately recognized with high affinity by the translation machinery. However, while the NTD recognizes the tRNA acceptor helix, shortened versions of MjPSTK (representing only 60% of the original size, in which the entire CTD, linker loop and an adjacent NTD helix are missing) are still active in vivo and in vitro, albeit with reduced activity compared to the full-length enzyme.

Articles - 3am1 mentioned but not cited (9)

  1. RNA folding pathways in stop motion. Bottaro S, Gil-Ley A, Bussi G. Nucleic Acids Res 44 5883-5891 (2016)
  2. Tertiary structure of bacterial selenocysteine tRNA. Itoh Y, Sekine S, Suetsugu S, Yokoyama S. Nucleic Acids Res 41 6729-6738 (2013)
  3. Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse. Ganichkin OM, Anedchenko EA, Wahl MC. PLoS One 6 e20032 (2011)
  4. C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec). Sherrer RL, Araiso Y, Aldag C, Ishitani R, Ho JM, Söll D, Nureki O. Nucleic Acids Res 39 1034-1041 (2011)
  5. Distinct Conformation of ATP Molecule in Solution and on Protein. Kobayashi E, Yura K, Nagai Y. Biophysics (Nagoya-shi) 9 1-12 (2013)
  6. RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. Antczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, Szachniuk M. BMC Bioinformatics 19 304 (2018)
  7. XGBPRH: Prediction of Binding Hot Spots at Protein⁻RNA Interfaces Utilizing Extreme Gradient Boosting. Deng L, Sui Y, Zhang J. Genes (Basel) 10 E242 (2019)
  8. Identification and Characterization of New RNA Tetraloop Sequence Families. Richardson KE, Adams MS, Kirkpatrick CC, Gohara DW, Znosko BM. Biochemistry 58 4809-4820 (2019)
  9. Toxin ζ Reduces the ATP and Modulates the Uridine Diphosphate-N-acetylglucosamine Pool. Moreno-Del Álamo M, Tabone M, Muñoz-Martínez J, Valverde JR, Alonso JC. Toxins (Basel) 11 E29 (2019)


Reviews citing this publication (4)

  1. Selenoproteins: molecular pathways and physiological roles. Labunskyy VM, Hatfield DL, Gladyshev VN. Physiol Rev 94 739-777 (2014)
  2. Naturally Occurring tRNAs With Non-canonical Structures. Krahn N, Fischer JT, Söll D. Front Microbiol 11 596914 (2020)
  3. The unique tRNASec and its role in selenocysteine biosynthesis. Serrão VHB, Silva IR, da Silva MTA, Scortecci JF, de Freitas Fernandes A, Thiemann OH. Amino Acids 50 1145-1167 (2018)
  4. Unconventional genetic code systems in archaea. Meng K, Chung CZ, Söll D, Krahn N. Front Microbiol 13 1007832 (2022)

Articles citing this publication (6)

  1. Computational identification of the selenocysteine tRNA (tRNASec) in genomes. Santesmasses D, Mariotti M, Guigó R. PLoS Comput Biol 13 e1005383 (2017)
  2. Insights into substrate promiscuity of human seryl-tRNA synthetase. Holman KM, Puppala AK, Lee JW, Lee H, Simonović M. RNA 23 1685-1699 (2017)
  3. Biophysical analysis of Arabidopsis protein-only RNase P alone and in complex with tRNA provides a refined model of tRNA binding. Pinker F, Schelcher C, Fernandez-Millan P, Gobert A, Birck C, Thureau A, Roblin P, Giegé P, Sauter C. J Biol Chem 292 13904-13913 (2017)
  4. Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Krutyhołowa R, Hammermeister A, Zabel R, Abdel-Fattah W, Reinhardt-Tews A, Helm M, Stark MJR, Breunig KD, Schaffrath R, Glatt S. Nucleic Acids Res 47 4814-4830 (2019)
  5. Trypanosomatid selenophosphate synthetase structure, function and interaction with selenocysteine lyase. da Silva MTA, Silva IRE, Faim LM, Bellini NK, Pereira ML, Lima AL, de Jesus TCL, Costa FC, Watanabe TF, Pereira HD, Valentini SR, Zanelli CF, Borges JC, Dias MVB, da Cunha JPC, Mittra B, Andrews NW, Thiemann OH. PLoS Negl Trop Dis 14 e0008091 (2020)
  6. Differential expression profile analysis of PSTK-regulated mRNAs in podocytes. Zheng D, Zhao Y, Liu L, Sun X, Xia Y, Sun L, Xie K. J Cell Biochem 120 8935-8948 (2019)


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