RF3 Induces Ribosomal Conformational Changes Responsible for Dissociation of Class I Release Factors

Gao, Haixiao; Zhou, Zhi-Hong; Rawat, U.; Huang, Chenhui; Bouakaz, Lamine; Wang, Chernhoe; Chen, Zhihong; Liu, Yuying; Zavialov, Andrey V.; Gursky, Richard; Sanyal, Suparna; Ehrenberg, Måns; Frank, Joachim; Song, Haiwei

doi:10.1016/j.cell.2007.03.050

Cited by 133 publications

(197 citation statements)

References 57 publications

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“…It was demonstrated that the affinity of RF1 for the post-termination complex is much higher than that of RF2. This would immediately suggest that RF1 is more difficult to recycle than RF2, which is also evident from the measurements of the spontaneous recycling time of the two release factors under the same experimental conditions (ϳ60 s for RF1 and 11 s for RF2) (28). In line with this argument, it has also been shown that RF1 is more dependent on RF3 for its recycling than is RF2 (13,28).…”

Section: Discussionsupporting

confidence: 66%

“…This would immediately suggest that RF1 is more difficult to recycle than RF2, which is also evident from the measurements of the spontaneous recycling time of the two release factors under the same experimental conditions (ϳ60 s for RF1 and 11 s for RF2) (28). In line with this argument, it has also been shown that RF1 is more dependent on RF3 for its recycling than is RF2 (13,28). The slow dissociation of RF1 after peptide release can have a significant consequence in a polysomic scenario where multiple ribosomes are lined up on a translating mRNA.…”

Section: Discussionmentioning

confidence: 77%

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Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

Korkmaz

Holm

Wiens

et al. 2014

Journal of Biological Chemistry

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101

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Background: Stop codon frequencies in 4684 bacterial genomes are analyzed. Results: With increasing genomic GC content, TAA% decreases, and TGA% increases reciprocally, but TAG% remains almost unchanged (ϳ20%). The TAG:TGA ratio matches well with the RF1:RF2 ratio. Conclusion: TAG is the minor stop codon, and expression of genes with TAG is correlated with the RF1 level. Significance: Our work establishes the correlation between stop codon frequency and RF1/RF2 abundance.

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Section: Discussionsupporting

confidence: 66%

Section: Discussionmentioning

confidence: 77%

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

Korkmaz

Holm

Wiens

et al. 2014

Journal of Biological Chemistry

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101

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“…1 and Fig. S3), in agreement with conclusions based on the results of numerous other approaches (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37). In some cases, multiconformer analysis may provide information about molecular motions that is not evident from TLS-derived B factor values alone.…”

Section: Resultssupporting

confidence: 78%

Multistart simulated annealing refinement of the crystal structure of the 70S ribosome

Коростелев

Laurberg

Noller

2009

Proc. Natl. Acad. Sci. U.S.A.

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A macromolecular X-ray crystal structure is usually represented as a single static model with a single set of temperature factors representing a simple approximation of motion and disorder of the structure. Multiconformer representations of small proteins have been shown to better describe anisotropic motion and disorder and improve the quality of their electron density maps. Here, we apply multistart simulated annealing crystallographic refinement to a 70S ribosome-RF1 translation termination complex that was recently solved at 3.2 Å resolution. The analysis improves the interpretability of the electron density map of this 2.5-MDa ribonucleoprotein complex and provides insights into its structural dynamics. We also used multistart refinement and conventional Fourier difference maps to address a recent study in which cross-crystal averaging between two crystal forms of the 70S ribosome was used to evaluate reported differences between two ribosome crystal structures solved at 2.8 and 3.7 Å resolution. Our analysis suggests that results obtained from cross-crystal averaging are inherently biased toward the higherresolution dataset.multistart refinement ͉ protein synthesis ͉ ribosome dynamics ͉ rRNA C rystallographic techniques and methods of structure determination have progressed rapidly in recent years, accompanied by an explosion in the amount of structural information about biological molecules and macromolecular assemblies. X-ray crystal structures have traditionally been represented by a single set of atomic coordinates accompanied by a set of temperature factors (B factors) to characterize atomic thermal motion. At most experimentally attainable resolutions, a spherical approximation for thermal motion is used, accounting only for the isotropic component of atomic displacement. It has been shown that the use of a static model with isotropic thermal parameters underestimates the total disorder and conformational variability of macromolecules (1-5). The limitation of the single-model approach is exemplified by several cases where high-resolution data are available. Nearly half the amino acid side chains and even some backbone atoms were found to have alternative conformations in the 0.54 Å structure of crambin and in the 1.0 Å structure of calmodulin (1, 6). To account for anharmonic contributions and conformational variability in X-ray structures, the use of an ensemble of models, as has long been standard practice in structure determination by NMR, has been suggested as a replacement for the traditional single-model approach (7). Multiconformer refinement has been implemented using both real-and reciprocal-space refinement approaches (2,3,(8)(9)(10)(11)(12)(13) and was demonstrated to yield improved agreement with diffraction data in most cases. In the case of molecular replacement phasing, electron density maps are often biased toward the search model; when a structure ensemble is used, however, model bias can be reduced significantly (14).In X-ray structures of the ribosome, the largest asymmetric struct...

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“…These two helices have been proposed to contact a common (unspecified) component of the ribosome (31). In RF3 a portion of the GЈ subdomain, including helix A GЈ , is present (32), but in IF2 the GЈ subdomain is completely missing, which suggests that these factors also may interact distinctly with L7/L12. This idea has precedent in other G proteins, which interact with GTPaseactivating proteins (GAPs) in structurally distinct ways (33).…”

Section: Discussionmentioning

confidence: 99%

Functional Interactions between the G′ Subdomain of Bacterial Translation Factor EF-G and Ribosomal Protein L7/L12

Nechifor

Murataliev

Wilson

2007

Journal of Biological Chemistry

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Protein L7/L12 of the bacterial ribosome plays an important role in activating the GTP hydrolytic activity of elongation factor G (EF-G), which promotes ribosomal translocation during protein synthesis. Previously, we cross-linked L7/L12 from two residues (209 and 231) flanking ␣-helix A G in the G subdomain of Escherichia coli EF-G. Here we report kinetic studies on the functional effects of mutating three neighboring glutamic acid residues (224, 228, and 231) to lysine, either singly or in combination. Two single mutations (E224K and E228K), both within helix A G , caused large defects in GTP hydrolysis and smaller defects in ribosomal translocation. Removal of L7/L12 from the ribosome strongly reduced the activities of wild type EF-G but had no effect on the activities of the E224K and E228K mutants. Together, these results provide evidence for functionally important interactions between helix A G of EF-G and L7/L12 of the ribosome.

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RF3 Induces Ribosomal Conformational Changes Responsible for Dissociation of Class I Release Factors

Cited by 133 publications

References 57 publications

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

Multistart simulated annealing refinement of the crystal structure of the 70S ribosome

Functional Interactions between the G′ Subdomain of Bacterial Translation Factor EF-G and Ribosomal Protein L7/L12

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