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Literature DB >> 19122150

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.

Elizabeth Villa¹, Jayati Sengupta, Leonardo G Trabuco, Jamie LeBarron, William T Baxter, Tanvir R Shaikh, Robert A Grassucci, Poul Nissen, Måns Ehrenberg, Klaus Schulten, Joachim Frank.

Abstract

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.

Entities: Chemical Gene Species

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Year: 2009 PMID： 19122150 PMCID： PMC2613361 DOI： 10.1073/pnas.0811370106

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

33 in total

1. Structure of the GDP-Pi complex of Gly203-->Ala gialpha1: a mimic of the ternary product complex of galpha-catalyzed GTP hydrolysis.

Authors: A M Berghuis; E Lee; A S Raw; A G Gilman; S R Sprang
Journal: Structure Date: 1996-11-15 Impact factor: 5.006

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.

1. Structure of the GDP-Pi complex of Gly203-->Ala gialpha1: a mimic of the ternary product complex of galpha-catalyzed GTP hydrolysis.

2. Helix unwinding in the effector region of elongation factor EF-Tu-GDP.

3. Nucleotide binding and GTP hydrolysis by elongation factor Tu from Thermus thermophilus as monitored by proton NMR.

4. An A to U transversion at position 1067 of 23 S rRNA from Escherichia coli impairs EF-Tu and EF-G function.

5. VMD: visual molecular dynamics.

6. An alpha to beta conformational switch in EF-Tu.

7. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation.

8. Limited proteolysis and amino acid replacements in the effector region of Thermus thermophilus elongation factor Tu.

9. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog.

10. Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.

1. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

2. Excited states of ribosome translocation revealed through integrative molecular modeling.

Review 3. Evolutionary optimization of speed and accuracy of decoding on the ribosome.

4. Optimization of speed and accuracy of decoding in translation.

5. Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.

6. Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection.

7. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.

8. Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome.

9. Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation.

10. Cryo-EM structure of the mammalian eukaryotic release factor eRF1-eRF3-associated termination complex.