2pjp › Citations

Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB.

Soler N, Fourmy D, Yoshizawa S
J Mol Biol 370 728-41 (2007)
Cited: 25 times
EuropePMC logo PMID: 17537456

Abstract

Elongation factor SelB is responsible for co-translational incorporation of selenocysteine (Sec) into proteins. The UGA stop codon is recoded as a Sec codon in the presence of a downstream mRNA hairpin. In prokaryotes, in addition to the EF-Tu-like N-terminal domains, a C-terminal extension containing four tandem winged-helix motifs (WH1-4) recognizes the mRNA hairpin. The 2.3-A resolution crystal structure of the Escherichia coli WH3/4 domains bound to mRNA with mutagenesis data reveal that the two WH motifs use the same structural elements to bind RNA. The structure together with the 2.6-A resolution structure of the WH1-4 domains from Moorella thermoacetica bound to RNA revealed that a salt bridge connecting WH2 to WH3 modules is disrupted upon mRNA binding. The results provide a structural basis for the molecular switch that may allow communication between tRNA and mRNA binding sites and illustrate how RNA acts as an activator of the switch. The structures show that tandem WH motifs not only provide an excellent scaffold for RNA binding but can also have an active role in the function of protein-RNA complexes.

Articles - 2pjp mentioned but not cited (12)

  1. DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. Tuszynska I, Bujnicki JM. BMC Bioinformatics 12 348 (2011)
  2. Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition. Iwakiri J, Tateishi H, Chakraborty A, Patil P, Kenmochi N. Nucleic Acids Res 40 3299-3306 (2012)
  3. Automated cryo-EM structure refinement using correlation-driven molecular dynamics. Igaev M, Kutzner C, Bock LV, Vaiana AC, Grubmüller H. Elife 8 e43542 (2019)
  4. Probing binding hot spots at protein-RNA recognition sites. Barik A, Nithin C, Karampudi NB, Karampudi NB, Mukherjee S, Bahadur RP. Nucleic Acids Res 44 e9 (2016)
  5. Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities. Guilhot-Gaudeffroy A, Froidevaux C, Azé J, Bernauer J. PLoS One 9 e108928 (2014)
  6. Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps. Kailasam S, Bhattacharyya D, Bansal M. BMC Res Notes 7 83 (2014)
  7. RNA-binding residues prediction using structural features. Ren H, Shen Y. BMC Bioinformatics 16 249 (2015)
  8. 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)
  9. Modelling and Recognition of Protein Contact Networks by Multiple Kernel Learning and Dissimilarity Representations. Martino A, De Santis E, Giuliani A, Rizzi A. Entropy (Basel) 22 E794 (2020)
  10. Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA. Soler N, Fourmy D, Yoshizawa S. Acta Crystallogr Sect F Struct Biol Cryst Commun 63 419-421 (2007)
  11. A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences. Agarwal A, Singh K, Kant S, Bahadur RP. Comput Struct Biotechnol J 20 3195-3207 (2022)
  12. Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools. Binet T, Padiolleau-Lefèvre S, Octave S, Avalle B, Maffucci I. BMC Bioinformatics 24 422 (2023)


Reviews citing this publication (3)

  1. From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins. Harami GM, Gyimesi M, Kovács M. Trends Biochem Sci 38 364-371 (2013)
  2. Challenges of site-specific selenocysteine incorporation into proteins by Escherichia coli. Fu X, Söll D, Sevostyanova A. RNA Biol 15 461-470 (2018)
  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)

Articles citing this publication (10)

  1. The pathway to GTPase activation of elongation factor SelB on the ribosome. Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H. Nature 540 80-85 (2016)
  2. The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA. Tan D, Zhou M, Kiledjian M, Tong L. Nat Struct Mol Biol 21 679-685 (2014)
  3. Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA. Ying BW, Fourmy D, Yoshizawa S. RNA 13 2042-2050 (2007)
  4. Roquin binding to target mRNAs involves a winged helix-turn-helix motif. Schuetz A, Murakawa Y, Rosenbaum E, Landthaler M, Heinemann U. Nat Commun 5 5701 (2014)
  5. The selenocysteine-specific elongation factor contains a novel and multi-functional domain. Gonzalez-Flores JN, Gupta N, DeMong LW, Copeland PR. J Biol Chem 287 38936-38945 (2012)
  6. Use of Baby Spinach and Broccoli for imaging of structured cellular RNAs. Okuda M, Fourmy D, Yoshizawa S. Nucleic Acids Res 45 1404-1415 (2017)
  7. Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB. Itoh Y, Sekine S, Yokoyama S. Nucleic Acids Res 43 9028-9038 (2015)
  8. Predicting RNA-binding residues from evolutionary information and sequence conservation. Huang YF, Chiu LY, Huang CC, Huang CK. BMC Genomics 11 Suppl 4 S2 (2010)
  9. A structure-based model for the prediction of protein-RNA binding affinity. Nithin C, Mukherjee S, Bahadur RP. RNA 25 1628-1645 (2019)
  10. Rational Design of Aptamer-Tagged tRNAs. Mukai T. Int J Mol Sci 21 E7793 (2020)


Related citations provided by authors (1)

  1. Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA.. Soler N, Fourmy D, Yoshizawa S Acta Crystallogr Sect F Struct Biol Cryst Commun 63 419-21 (2007)

Quick links