Mutations in the conserved P loop perturb the conformation of two structural elements in the peptidyl transferase center of 23 s ribosomal RNA 1 1Edited by D. Draper

Gregory, Steven T.; Dahĺberg, Albert E.

doi:10.1006/jmbi.1998.2410

Cited by 19 publications

(12 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The bases that comprise the clusters are as follows: (i) U2474, C2475, and A2476; (ii) U2492, U2493, and G2494; (iii) G2553, U2554, U2555, and C2556; (iv) A2560, U2561, U2562, U2563, and A2564; and (v) U2585, U2586, A2587, and G2588. Among these, the positions G2553, U2555, U2492, and U2493 are known to be required for tRNA binding and translational fidelity (19,28,29). The stops were identical in positions and relative intensities for BCA, LDH, MDH, and lysozyme and were absent when RNA was irradiated in the presence of native proteins (data not shown) or in the absence of any protein ( Fig.…”

Section: Resultsmentioning

confidence: 80%

Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions

et al. 2008

View full text Add to dashboard Cite

The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.Ribosomes from various sources have shown protein-folding activity in vitro (1,13,14,23). This activity was tested on more than a dozen proteins with various tertiary structures and organizations (1,7,14,20). The activity was found later to be present in the large ribosomal subunit, and on stripping ribosomes of their proteins, it could be assigned to the peptidyl transferase center (PTC) in the larger RNA of the large subunit (8,11,30,35). In Escherichia coli and in other eubacteria in general, the PTC is in domain V (U2016 to G2625 of E. coli) of 23S rRNA.If the same RNA can fold a large number of proteins which are structurally unrelated, the question of specificity arises in the interaction of the unfolded proteins with the RNA. Here we have deciphered the RNA-protein interactions at the nucleotide-amino acid level.To locate the interacting nucleotides of domain V, we used primer extension analysis and determined the positions where the extensions were blocked. We found that the same set of nucleotides interacts with four different proteins tested: bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), and chicken egg white lysozyme. Using matrix-assisted laser desorption ionization-time of flight/time of flight (MALDI-TOF/TOF), we also tested whether the RNA interacted with specific amino acids. In the two proteins tested, BCA and lysozyme, the amino acids involved were specific for each protein and could even be identical between the two proteins. The disposition of the amino acids on the three-dimensional structure shared some common features. The RNA-protein interactions thus appear to have significant specificity. MATERIALS AND METHODSIn vitro synthesis of domain V of E. coli 23S rRNA. The rRNA gene fragment containing domain V was cloned in vector pTZ57R/T (Fermentas) under the control of a T7 promoter. The presence of the domain in selected clones was verified by DNA sequencing. An EcoRI restriction site, just downstream of the domain, was used to linearize the plasmid, and RNA was synthesized using ...

show abstract

Section: Resultsmentioning

confidence: 80%

Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions

et al. 2008

View full text Add to dashboard Cite

show abstract

“…Again, an emphasis should be made that the reactivity changes observed here are not of the allor-none nature. Mutations in the P-loop 27 have previously been found to affect the conformation of the tip of helix 91, while a mutation in helix 39 affected both the P-loop and nucleotide residues surrounding helix 89. 28 It is likely that DB1a and the set of other mutations shift equilibrium between the conformers of the ribosome, rather than destroy some structural elements completely.…”

Section: Discussionmentioning

confidence: 98%

The Conserved A-site Finger of the 23S rRNA: Just One of the Intersubunit Bridges or a Part of the Allosteric Communication Pathway?

Сергиев

Kiparisov

Burakovsky

et al. 2005

Journal of Molecular Biology

View full text Add to dashboard Cite

“…Indeed, chemical probing studies showed that mutation at G2252 alters the conformation of the A loop, especially of base G2553 in 23 S rRNA. 31 This may represent a shift in the conformational equilibrium towards the uninduced state in the mutant ribosomes. However, an intact aminoacyl-tRNA in the A site may shift the equilibrium back to the induced state and properly orient the P site tRNA for peptide bond formation.…”

Section: Discussionmentioning

confidence: 99%

A Conserved Base-pair between tRNA and 23 S rRNA in the Peptidyl Transferase Center Is Important for Peptide Release

Feinberg

Joseph²

2006

Journal of Molecular Biology

View full text Add to dashboard Cite

Mutations in the conserved P loop perturb the conformation of two structural elements in the peptidyl transferase center of 23 s ribosomal RNA 1 1Edited by D. Draper

Cited by 19 publications

References 27 publications

Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions

Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions

The Conserved A-site Finger of the 23S rRNA: Just One of the Intersubunit Bridges or a Part of the Allosteric Communication Pathway?

A Conserved Base-pair between tRNA and 23 S rRNA in the Peptidyl Transferase Center Is Important for Peptide Release

Contact Info

Product

Resources

About