Visualizing tmRNA Entry into a Stalled Ribosome

Valle, Mikel; Gillet, Reynald; Kaur, Sukhjit; Henne, Anke; Ramakrishnan, V.; Frank, Joachim

doi:10.1126/science.1081798

Cited by 136 publications

(125 citation statements)

References 36 publications

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“…cryo-EM studies of the complex of tmRNA interacting with the ribosome in the pre-initiation stage in which the tRNA-like region of tmRNA remains in the complex with elongation factor Tu-GDP placed pk1 in the decoding center of ribosome. According to the cryo-EM model, another pseudoknot forms an arch-like structure in the 30 S subunit (17). This structure agrees well with our hypothesis.…”

Section: Discussionsupporting

confidence: 81%

“…Recently we proposed a hypothetical model describing how tmRNA may first enter and than pass through the ribosome (19). The predicted conformation of tmRNA at the initial stage of its interaction with the ribosome was confirmed by cryo-EM (17). According to our model, several structural elements of tmRNA should remain intact during the passage of tmRNA through the ribosome, and they should be located on the surface of ribosome (19).…”

mentioning

confidence: 99%

“…SmpB was also found to be the partner of tmRNA on entering the ribosome during the pre-accommodation stage (17). Comparison of the x-ray crystal structure of a ribonucleoprotein complex that includes a tmRNA fragment and SmpB (18) with cryo-electron microscopic (cryo-EM) data for tmRNA⅐SmpB complex entering the ribosome (17) shows that SmpB protein may change its position within the tmRNA.…”

mentioning

confidence: 99%

“…The interaction of tmRNA with the ribosome was studied by cryo-EM only at the pre-accommodation stage (17). Little is known about such interactions at later stages of trans-translation.…”

mentioning

confidence: 99%

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Stepping Transfer Messenger RNA through the Ribosome

Shpanchenko

Zvereva

Ivanov

et al. 2005

Journal of Biological Chemistry

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Section: Discussionsupporting

confidence: 81%

mentioning

confidence: 99%

mentioning

confidence: 99%

“…The interaction of tmRNA with the ribosome was studied by cryo-EM only at the pre-accommodation stage (17). Little is known about such interactions at later stages of trans-translation.…”

mentioning

confidence: 99%

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Stepping Transfer Messenger RNA through the Ribosome

Shpanchenko

Zvereva

Ivanov

et al. 2005

Journal of Biological Chemistry

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“…The E. coli 23 S rRNA sequence between 1934 and 1949 is highly complementary (14 of 16 nucleotides) to the sequence in the tRNA-like domain of tmRNA, strongly indicating that it has the potential to base pair with the tmRNA. A cryo-EM structure of the ribosome-tmRNA complex places the tmRNA in a location proximal to U1939 (52). These observations suggest that the region around U1939 has a role in tRNA and tmRNA binding.…”

Section: Discussionmentioning

confidence: 82%

Redox Reactions of the Iron-Sulfur Cluster in a Ribosomal RNA Methyltransferase, RumA

Agarwalla

Stroud

Gaffney

2004

Journal of Biological Chemistry

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RumA, an S-adenosyl-L-methionine-dependent methyltransferase specifically catalyzes the methylation of U1939 of 23 S ribosomal RNA to yield 5-methyluridine (m 5 U) 1 or ribothymidine (1). This enzyme was found to contain a [4Fe-4S] cluster, a prosthetic group usually not associated with methyltransferase enzymes. The x-ray structure of RumA revealed that the cluster is located in the RNA binding domain of the threedomain protein (2). It is held by four Cys-iron bonds provided by Cys 81 , Cys 87 , Cys 90 , and Cys 162 and is buried in a largely hydrophobic region, but one of its sulfur atoms is quite exposed to solvent. The closest distance between the cluster and the sulfur of the catalytic nucleophile, Cys 389 , is ϳ19 Å. RumA is a member of a growing list of nucleic acid modifying enzymes where the function of the iron-sulfur (FeS) cluster remains enigmatic.The reaction mechanism of m 5 U methyltransferases is similar to that of thymidylate synthase, and has been studied mainly employing the tRNA m 5 U54 methyltransferase, TrmA (3-5). It involves Michael addition of the catalytic Cys to carbon 6 (C-6) of pyrimidine, which activates C-5 for a nucleophilic attack on the methyl group of S-adenosyl-L-methionine. Following the methyl transfer, the enzyme is resolved by abstraction of a proton from C-5 and ␤-elimination. TrmA, as well as DNA and RNA 5-methylcytidine methyltransferases, which employ a similar catalytic mechanism (6), do not posses an FeS cluster or any other prosthetic group. Lack of a redox step in the catalytic mechanism, and absence of the cluster in enzymes that employ a similar mechanism preclude a direct role for [4Fe-4S] cluster in the RumA-catalyzed reaction.Two features distinguish the FeS cluster in RumA from the clusters in a different class of S-adenosyl-L-methionine-dependent enzymes that proceed by free radical mechanisms. The RumA cluster is ligated by 4 cysteines and the iron-binding sequence motif is CX 5 CX 2 CX n C. In contrast, the radical Sadenosyl-L-methionine enzymes, of which MiaB (7) and biotin synthase (8) are examples, have a [4Fe-4S] cluster built of a CX 3 CX 2 C sequence that leaves one iron of the cluster free to participate in catalysis. MiaB is a member of a family of enzymes catalyzing addition of sulfur to tRNA bases (9). The FeS sequence motifs in the DNA repair enzymes, endonuclease III (10) and MutY (11), are CX 6 CX 2 CX 5 C, somewhat similar to the RumA sequence. Although the FeS clusters in these enzymes are usually regarded as structural, recently it was shown that the redox potential of MutY is altered by DNA binding and that a change in charge of the [4Fe-4S] 3ϩ/2ϩ cluster might alter its affinity for DNA (12).The redox potentials of [4Fe-4S] clusters vary widely (13-16). Of particular interest in many contemporary studies of FeS proteins is understanding the factors that influence the potentials, and thus functions, of these clusters (17,18). Proteins with four Cys-iron bonds to the [4Fe-4S] cluster fall into two general redox groups, ones with an accessib...

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