The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of <i>Escherichia coli</i>
 ribosome

Burakovsky, Dmitry E.; Сергиев, Петр В.; Steblyanko, Maria; Konevega, Andrey L.; Bøgdanov, A.; Dontsova, Olga А.

doi:10.1016/j.febslet.2011.08.030

Cited by 18 publications

(17 citation statements)

References 25 publications

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“…Finally, the CTD occupies the A site of the 50S subunit, and its β-turn (residues 527-532) interacts with H89 (Fig. S4E), which is an important element of ribosome because it connects the PTC and the elongation factor binding site (33). Furthermore, the distal loop residues (552-555 and beyond 555) appear to touch the hairpin loop of H92 at the PTC.…”

Section: Resultsmentioning

confidence: 99%

Structure of BipA in GTP form bound to the ratcheted ribosome

Kumar

Chen

Ero

et al. 2015

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

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BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3′,5′-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.

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Section: Resultsmentioning

confidence: 99%

Structure of BipA in GTP form bound to the ratcheted ribosome

Kumar

Chen

Ero

et al. 2015

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

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“…The hybrid corridor is analogous to the accommodation corridor that we previously identified, 46 for which the constituent molecular interactions have been experimental corroborated. [65][66][67][68][69] …”

Section: Cca Movement Is Associated With An Intermediate Ensemble Andmentioning

confidence: 98%

Simulating movement of tRNA through the ribosome during hybrid-state formation

Whitford

Sanbonmatsu

2013

The Journal of Chemical Physics

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Biomolecular simulations provide a means for exploring the relationship between flexibility, energetics, structure, and function. With the availability of atomic models from X-ray crystallography and cryoelectron microscopy (cryo-EM), and rapid increases in computing capacity, it is now possible to apply molecular dynamics (MD) simulations to large biomolecular machines, and systematically partition the factors that contribute to function. A large biomolecular complex for which atomic models are available is the ribosome. In the cell, the ribosome reads messenger RNA (mRNA) in order to synthesize proteins. During this essential process, the ribosome undergoes a wide range of conformational rearrangements. One of the most poorly understood transitions is translocation: the process by which transfer RNA (tRNA) molecules move between binding sites inside of the ribosome. The first step of translocation is the adoption of a "hybrid" configuration by the tRNAs, which is accompanied by large-scale rotations in the ribosomal subunits. To illuminate the relationship between these rearrangements, we apply MD simulations using a multi-basin structure-based (SMOG) model, together with targeted molecular dynamics protocols. From 120 simulated transitions, we demonstrate the viability of a particular route during P/E hybrid-state formation, where there is asynchronous movement along rotation and tRNA coordinates. These simulations not only suggest an ordering of events, but they highlight atomic interactions that may influence the kinetics of hybrid-state formation. From these simulations, we also identify steric features (H74 and surrounding residues) encountered during the hybrid transition, and observe that flexibility of the single-stranded 3'-CCA tail is essential for it to reach the endpoint. Together, these simulations provide a set of structural and energetic signatures that suggest strategies for modulating the physical-chemical properties of protein synthesis by the ribosome.

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“…The helix H89 resides at the 60S subunit surface facing the 40S subunit and extends from the PTC ring (Anger et al 2013). According to numerous data obtained with bacterial ribosomes (e.g., see O'Connor and Dahlberg 1995;La Teana et al 2001;Burakovsky et al 2011), H89 is involved in different steps of the translation process. In eukaryotes, this helix is implicated in interaction of the ribosomes with eIF5B (Unbehaun et al 2007).…”

Section: Regions Of Rrnas Implicated In the Conformational Rearrangemmentioning

confidence: 99%

Chemical footprinting reveals conformational changes of 18S and 28S rRNAs at different steps of translation termination on the human ribosome

Bulygin

Bartuli

Malygin

et al. 2015

RNA

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Translation termination in eukaryotes is mediated by release factors: eRF1, which is responsible for stop codon recognition and peptidyl-tRNA hydrolysis, and GTPase eRF3, which stimulates peptide release. Here, we have utilized ribose-specific probes to investigate accessibility of rRNA backbone in complexes formed by association of mRNA-and tRNA-bound human ribosomes with eRF1•eRF3•GMPPNP, eRF1•eRF3•GTP, or eRF1 alone as compared with complexes where the A site is vacant or occupied by tRNA. Our data show which rRNA ribose moieties are protected from attack by the probes in the complexes with release factors and reveal the rRNA regions increasing their accessibility to the probes after the factors bind. These regions in 28S rRNA are helices 43 and 44 in the GTPase associated center, the apical loop of helix 71, and helices 89, 92, and 94 as well as 18S rRNA helices 18 and 34. Additionally, the obtained data suggest that eRF3 neither interacts with the rRNA ribosephosphate backbone nor dissociates from the complex after GTP hydrolysis. Taken together, our findings provide new information on architecture of the eRF1 binding site on mammalian ribosome at various translation termination steps and on conformational rearrangements induced by binding of the release factors.

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The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome

Cited by 18 publications

References 25 publications

Structure of BipA in GTP form bound to the ratcheted ribosome

Structure of BipA in GTP form bound to the ratcheted ribosome

Simulating movement of tRNA through the ribosome during hybrid-state formation

Chemical footprinting reveals conformational changes of 18S and 28S rRNAs at different steps of translation termination on the human ribosome

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