Structure of the 70 S ribosome: implications for movement

Noller, Harry F.; Baucom, Albion

doi:10.1042/bst0301159

Cited by 24 publications

(18 citation statements)

References 1 publication

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The crystal structure of the 70 S ribosome complexed with tRNA and mRNA showed that the C-terminal ␣-helix of S7, close to the region of interaction with S11, contacts the anticodon loop of the E-site-bound tRNA (5,12). In agreement with the x-ray studies, S7 and S11 were cross-linked to the anticodon loop of the E-site bound tRNA (31,32).…”

supporting

confidence: 71%

“…For example, x-ray and cryo-EM studies clearly showed that such changes occur upon subunit association, binding of aminoacyl-tRNA (aatRNA) or factors, and during translocation (5, 12, 24 -30). Thus, the S7-S11 interaction, which constitutes a contact between the 30 S head and platform, likely participates in the conformational changes undergone by the 30 S, breaking and re-forming during translation.The crystal structure of the 70 S ribosome complexed with tRNA and mRNA showed that the C-terminal ␣-helix of S7, close to the region of interaction with S11, contacts the anticodon loop of the E-site-bound tRNA (5,12). In agreement with the x-ray studies, S7 and S11 were cross-linked to the anticodon loop of the E-site bound tRNA (31, 32).…”

supporting

confidence: 71%

“…The elucidation of the crystal structure of the prokaryotic ribosome has led to a major progress in understanding its function (1)(2)(3)(4)(5)(6)(7). Analysis of the ribosome structure combined with a wealth of biochemical data clearly showed that ribosomal RNA (rRNA) is the key player in the functions of the ribosome, and it is currently assumed that the main task of the ribosomal proteins is to help and stabilize rRNA folding and to facilitate conformational changes in rRNA (8 -10).…”

mentioning

confidence: 99%

See 2 more Smart Citations

A Functional Interaction between Ribosomal Proteins S7 and S11 within the Bacterial Ribosome

Robert¹,

Brakier‐Gingras

2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

In this study, we used site-directed mutagenesis to disrupt an interaction that had been detected between ribosomal proteins S7 and S11 in the crystal structure of the bacterial 30 S subunit. This interaction, which is located in the E site, connects the head of the 30 S subunit to the platform and is involved in the formation of the exit channel through which passes the 30 S-bound messenger RNA. Neither mutations in S7 nor mutations in S11 prevented the incorporation of the proteins into the 30 S subunits but they perturbed the function of the ribosome. In vivo assays showed that ribosomes with either mutated S7 or S11 were altered in the control of translational fidelity, having an increased capacity for frameshifting, readthrough of a nonsense codon and codon misreading. Toeprinting and filter-binding assays showed that 30 S subunits with either mutated S7 or S11 have an enhanced capacity to bind mRNA. The effects of the S7 and S11 mutations can be related to an increased flexibility of the head of the 30 S, to an opening of the mRNA exit channel and to a perturbation of the proposed allosteric coupling between the A and E sites. Altogether, our results demonstrate that S7 and S11 interact in a functional manner and support the notion that protein-protein interactions contribute to the dynamics of the ribosome.The ribosome is the cellular machinery responsible for protein synthesis in all living organisms. The elucidation of the crystal structure of the prokaryotic ribosome has led to a major progress in understanding its function (1-7). Analysis of the ribosome structure combined with a wealth of biochemical data clearly showed that ribosomal RNA (rRNA) is the key player in the functions of the ribosome, and it is currently assumed that the main task of the ribosomal proteins is to help and stabilize rRNA folding and to facilitate conformational changes in rRNA (8 -10). However, a growing list of examples suggests that ribosomal proteins directly participate to protein synthesis. The x-ray structure of the ribosome reveals that S12 is part of the decoding site (Refs. 11 and 12, reviewed in Ref. 13). It also shows that the 30 S proteins S13, S15, and the 50S proteins L2, L5, L14, L19 are involved in intersubunit bridges, while the 30 S proteins S9, S13, and the 50 S proteins L1, L5, L33 interact with tRNAs, suggesting that they could participate in the translocation step (12). Studies in solution also point to a role for the ribosomal proteins, such as an involvement in mRNA binding for S1 (14 -16), a participation in peptidyl transferase activity for L2 (17-19) and the prevention of mRNA slippage for L9 (20).Several protein-protein interactions were identified in the crystal structure of the 30 S subunit (21, 22) but, so far, only the interaction between proteins S4 and S5 has been directly related to a particular ribosome function, that is the control of translational fidelity. Indeed, mutations that disrupt the S4-S5 interaction decrease translational accuracy (23,24). Among the other protein-protein inter...

show abstract

supporting

confidence: 71%

supporting

confidence: 71%

mentioning

confidence: 99%

See 1 more Smart Citation

A Functional Interaction between Ribosomal Proteins S7 and S11 within the Bacterial Ribosome

Robert¹,

Brakier‐Gingras

2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…The pivoting or nodding of the head in different directions has been observed by both cryoelectron microscopy and comparison of crystallographic structures Gabashvili et al 1999;Frank and Agrawal 2000;Noller and Baucom 2001;Ogle et al 2002). The head of the 30S subunit seemed to rotate or bent by 90°i n the late stages of assembly or initiation complex formation, as studied by Monte Carlo simulation , but there has been scant experimental support for these motions.…”

Section: Discussionmentioning

confidence: 99%

Ribosomal dynamics inferred from variations in experimental measurements

Gabashvili

Whirl‐Carrillo²,

Bada³

et al. 2003

RNA

View full text Add to dashboard Cite

The crystal structures of the ribosome reveal remarkable complexity and provide a starting set of snapshots with which to understand the dynamics of translation. To augment the static crystallographic models with dynamic information present in crosslink, footprint, and cleavage data, we examined 2691 proximity measurements and focused on the subset that was apparently incompatible with >40 published crystal structures. The measurements from this subset generally involve regions of the structure that are functionally conserved and structurally flexible. Local movements in the crystallographic states of the ribosome that would satisfy biochemical proximity measurements show coherent patterns suggesting alternative conformations of the ribosome. Three different types of data obtained for the two subunits display similar "mismatching" patterns, suggesting that the signals are robust and real. In particular, there is an indication of coherent motion in the decoding region within the 30S subunit and central protuberance and surrounding areas of the 50S subunit. Directions of rearrangements fluctuate around the proposed path of tRNA translocation and the plane parallel to the interface of the two subunits. Our results demonstrate that systematic combination and analysis of noisy, apparently incompatible data sources can provide biologically useful signals about structural dynamics.

show abstract

“…www.rnajournal.org at the top of the helix 44 (Noller and Baucom 2002), as does the movement of helix 44 in response to the binding of ribosome release factor to 70S ribosomes (Agrawal et al 2004).…”

Section: Asl-16s Rrna Photocrosslinkingmentioning

confidence: 99%

Photolabile anticodon stem–loop analogs of tRNA^Phe as probes of ribosomal structure and structural fluctuation at the decoding center

Druzina

Cooperman²

2004

RNA

View full text Add to dashboard Cite

With the recent availability of high-resolution structures of bacterial ribosomes, studies of ribosome-catalyzed protein biosynthesis are now focusing on the nature of conformational changes that occur as the ribosome exerts its complex catalytic function. Photocrosslinking can be relevant for this purpose by providing clues to ribosomal structural fluctuations and dynamics. Here we describe crosslinking experiments on 70S ribosomes using two photolabile anticodon stem-loop derivatives of Escherichia coli tRNA Phe carrying a 4-thiouridine in either position 33 or 37 and denoted Ph-ASLs. One or both of these Ph-ASLs bind to the tRNA A-, P-, and E-sites on the ribosome, with both binding to and photocrosslinking from the E-site showing strong dependence on the presence of a tRNA in the P-site. Both Ph-ASLs crosslink to the extreme 3-end of 16S rRNA from both the P-and E-sites, providing direct confirmatory evidence in solution for the folding back of the 3-end toward the decoding region. This suggests that the 3-end of 16S rRNA may act as a switch in controlling mRNA access to the decoding center, a phenomenon of potential relevance for the translation of leaderless mRNA. E-site bound Ph-ASLs also form photocrosslinks to nucleotides 1395-1398, 1399-1400, and 1491-1494 at the top of helix 44 of 16S rRNA, indicating movement of the decoding center from a position between the A-and P-sites seen in the crystal structure to one neighboring the E-site.

show abstract

Structure of the 70 S ribosome: implications for movement

Cited by 24 publications

References 1 publication

A Functional Interaction between Ribosomal Proteins S7 and S11 within the Bacterial Ribosome

A Functional Interaction between Ribosomal Proteins S7 and S11 within the Bacterial Ribosome

Ribosomal dynamics inferred from variations in experimental measurements

Photolabile anticodon stem–loop analogs of tRNA^Phe as probes of ribosomal structure and structural fluctuation at the decoding center

Contact Info

Product

Resources

About

Structure of the 70 S ribosome: implications for movement

Cited by 24 publications

References 1 publication

A Functional Interaction between Ribosomal Proteins S7 and S11 within the Bacterial Ribosome

A Functional Interaction between Ribosomal Proteins S7 and S11 within the Bacterial Ribosome

Ribosomal dynamics inferred from variations in experimental measurements

Photolabile anticodon stem–loop analogs of tRNAPhe as probes of ribosomal structure and structural fluctuation at the decoding center

Contact Info

Product

Resources

About

Photolabile anticodon stem–loop analogs of tRNA^Phe as probes of ribosomal structure and structural fluctuation at the decoding center