A new model for the three-dimensional folding of Escherichia coli 16 s ribosomal RNA. III † . The topography of the functional centre 1 †Paper II in this series is an accompanying paper, Mueller &amp; Brimacombe (1997b). 1Edited by D. E. Draper

Mueller, Florian; Stark, Holger; Heel, Marin van; Rinke-Appel, Jutta; Brimacombe, Richard

doi:10.1006/jmbi.1997.1212

Cited by 74 publications

(12 citation statements)

References 68 publications

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“…This base pairing results in a short double helix that we call the codon-anticodon helix. Data from chemical protection (13), cross-linking (14), and genetic analysis (15) suggest that the decoding site is a region around the ribosomal A site that includes helix 44, the 530 loop, and helix 34 of 16S RNA, which are now known from the high-resolution structure of the 30S subunit to be close to one another (16,17).…”

mentioning

confidence: 99%

Recognition of Cognate Transfer RNA by the 30 S Ribosomal Subunit

Ogle

Brodersen

Clemons

et al. 2001

Science

1,117

1,211

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Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.During protein synthesis, the ribosome catalyzes the sequential addition of amino acids to a growing polypeptide chain, using mRNA as a template and aminoacylated tRNAs (aatRNAs) as substrates. Correct base pairing between the three bases of the codon on mRNA and those of the anticodon of the cognate aatRNA dictates the sequence of the polypeptide chain. Discrimination against noncognate tRNA, which generally has two or three mismatches in the base pairing, can be accounted for by the difference in the free energy of base pairing to the codon compared with cognate tRNA. For near-cognate tRNA, which usually involves a single mismatch, the free-energy difference in base pairing compared with cognate tRNA would predict an error rate that is one to two orders of magnitude higher than the actual error rate of protein synthesis (1), and it has long been recognized that the ribosome must improve the accuracy of protein synthesis by discriminating against near-cognate tRNAs (2). This discrimination involves the 30S subunit, which binds mRNA and the anticodon stem-loop (ASL) of tRNA.At the beginning of the elongation cycle, which involves the addition of a new amino acid to a growing polypeptide chain, the aatRNA is presented to the ribosome as a ternary complex with elongation factor Tu (EF-Tu) and guanosine triphosphate (GTP). The selection of cognate tRNA is believed to occur in two stages-an initial recognition step and a proofreading step-that are separated by the irreversible hydrolysis of GTP by EF-Tu (3-6). In this scheme, the discrimination energy inherent in codon-anticodon base pairing is exploited twice to achieve the necessary accuracy. Recent experiments suggest that the binding of cognate rather than near-cognate tRNA results in higher rates of both GTP hydrolysis by EF-Tu, and accommodation, a process in which the acceptor arm of the aa-tRNA swings into the peptidyl transferase site after its release from EF-Tu (7,8). In both steps, the higher rate is proposed to be the result of structural changes in the ribosome induced by cognate tRNA. In the context of proofreading mechanisms alone, it is unclear whether additional structural discrimination by the ribosome, ...

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mentioning

confidence: 99%

Recognition of Cognate Transfer RNA by the 30 S Ribosomal Subunit

Ogle

Brodersen

Clemons

et al. 2001

Science

1,117

1,211

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“…Nucleotide U1052 was cross-linked to the 3Ј end of the mRNA codon in the A site (41), whereas A1196 was cross-linked to mRNA residues ϩ8 and ϩ9 (42). According to the crystal structures of functional ribosome complexes, C1054 and A1196 are in contact with the mRNA-tRNA complex (3,43), whereas other residues are not and may serve as a 3Ј-boundary for the A site (44,45). Genetic studies examined the influence of mutations at a number of positions in h34 (1054, 1057, 1058, 1199, 1200, 1202, and 1203) on stop-codon readthrough and frameshifting (14), whereas mutations in positions studied in this work (1109, 1191, 1201/961) were not tested.…”

Section: Effects Of Mutations On 30 S Subunit Structure and Associatimentioning

confidence: 99%

“…The effects of the mutations can be explained by changes in (i) the interactions of h34 with mRNA and the presumed function of h34 as mRNA boundary (44,45) and/or (ii) the stability of the mRNA-tRNA complex at the state at which frameshifting may occur (46). Because A1191 is located in the center of the junction formed by h34 and h35/36/38, mutations in h34 may not only change the local structure in this region but also the global structure of the 30 S subunit by altering the relative orientation of the head and the body of the subunit.…”

Section: Effects Of Mutations On 30 S Subunit Structure and Associatimentioning

confidence: 99%

Involvement of Helix 34 of 16 S rRNA in Decoding and Translocation on the Ribosome

Kubarenko

Сергиев

Wintermeyer

et al. 2006

Journal of Biological Chemistry

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Helix 34 of 16 S rRNA is located in the head of the 30 S ribosomal subunit close to the decoding center and has been invoked in a number of ribosome functions. In the present work, we have studied the effects of mutations in helix 34 both in vivo and in vitro. Several nucleotides in helix 34 that are either highly conserved or form important tertiary contacts in 16 S rRNA (U961, C1109, A1191, and A1201) were mutated, and the mutant ribosomes were expressed in the Escherichia coli MC250 ⌬7 strain that lacks all seven chromosomal rRNA operons. Mutations at positions A1191 and U961 reduced the efficiency of subunit association and resulted in structural rearrangements in helix 27 (position 908) and helix 31 (position 974) of 16 S rRNA. All mutants exhibited increased levels of frameshifting and nonsense readthrough. The effects on frameshifting were specific in that ؊1 frameshifting was enhanced with mutant A1191G and ؉1 frameshifting with the other mutants. Mutations of A1191 moderately (ϳ2-fold) inhibited tRNA translocation. No significant effects were found on efficiency and rate of initiation, misreading of sense codons, or binding of tRNA to the E site. The data indicate that helix 34 is involved in controlling the maintenance of the reading frame and in tRNA translocation.

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“…Given this idea, we examined a variety of molecular models for the 30S ribosomal subunit to determine the presence of knots (9)(10)(11)(12)(13)(14)(15)(16). These models fall into two primary categories, those built by hand (9,10,14-16) and those built using computer automated algorithms (11-13).…”

Section: Introductionmentioning

confidence: 99%

To Knot or Not to Knot? Examination of 16S Ribosomal RNA Models

VanLoock

Harris

Harvey

1998

Journal of Biomolecular Structure and Dynamics

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The presence of topological knots in large RNA structures is highly unlikely given that 1) no RNA structures determined thus far contain topological knots, 2) secondary structure maps for most RNA molecules are knot free, 3) there are no known RNA topoisomerases, and 4) it is difficult to imagine how knots could be formed specifically and uniquely during transcription. Since native RNA structures probably lack topological knots, models of these RNA molecules should be free of knots as well. Therefore, we have examined four existing models for the 30S ribosomal subunit to determine if any of the three domains of the 16S rRNA molecule is knotted. We found that all but one model had at least one knotted domain. We conclude that models of large RNA molecules should be examined for knotting before publication.

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A new model for the three-dimensional folding of Escherichia coli 16 s ribosomal RNA. III † . The topography of the functional centre 1 †Paper II in this series is an accompanying paper, Mueller & Brimacombe (1997b). 1Edited by D. E. Draper

Cited by 74 publications

References 68 publications

Recognition of Cognate Transfer RNA by the 30 S Ribosomal Subunit

Recognition of Cognate Transfer RNA by the 30 S Ribosomal Subunit

Involvement of Helix 34 of 16 S rRNA in Decoding and Translocation on the Ribosome

To Knot or Not to Knot? Examination of 16S Ribosomal RNA Models

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