Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet

Schmitt, Emmanuelle; Panvert, Michel; Blanquet, Sylvain; Mechulam, Yves

doi:10.1093/emboj/17.23.6819

Cited by 135 publications

(135 citation statements)

References 36 publications

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“…The crystal structure of the complex of E. coli MetRS with tRNA Met is not available, although the structures of tRNA Met (26) and MetRS (27,28) are available. Hence, we modeled the structure of MetRStRNA f Met complex by using the Aquifex aeolicus (29) as a template.…”

Section: Resultsmentioning

confidence: 99%

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

Ghosh

Vishveshwara

2007

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

229

288

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The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by Ϸ70 Å in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS ؉ activated methonine) and (MetRS ؉ tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through longdistance communication.dynamic cross-correlations ͉ methionyl-AMP ͉ protein structure network ͉ shortest pathways of communication ͉ stacking A crucial step in the translation of the genetic code is the aminoacylation of tRNA, which involves the molecular recognition between the aminoacyl-tRNA synthetases (aaRS) and their cognate tRNA. Each synthetase consists of the catalytic domain and the anticodon domain that are separated by Ϸ70 Å. Each tRNA connects these two regions with its anticodon and the acceptor stems. The mechanism of differentiations between cognate and noncognate tRNAs depends on contacts of anticodon domain of synthetase and anticodon stem of tRNA. The efficiency of the selection mechanism controls the overall accuracy of protein synthesis (1, 2). Recognition of the protein (aaRS) and the tRNA is explained by using the induced-fit mechanism, which suggests conformational changes in protein, tRNA, or both, leading to the final bound complex (3). However, the details of communication between the anticodon region and the aminoacylation region are less understood.In all living cells, protein synthesis starts with methionine.

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Section: Resultsmentioning

confidence: 99%

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

Ghosh

Vishveshwara

2007

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

229

288

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“…5. The general structure of MTFs consisting of two domains that are separated by a linker region seems to be retained in trypanosomes (22,23). Interestingly, the linker region (at position 313-368) is longer than in any of the other enzymes.…”

Section: Discussionmentioning

confidence: 99%

Eukaryotic-type elongator tRNA ^Met of Trypanosoma brucei becomes formylated after import into mitochondria

Tan

Bochud-Allemann

Horn

et al. 2002

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

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The mitochondrion of Trypanosoma brucei lacks tRNA genes. Its translation system therefore depends on the import of cytosolic, nucleus-encoded tRNAs. Thus, most trypanosomal tRNAs function in both the cytosol and the mitochondrion, and all are of the eukaryotic type. This is also the case for the elongator tRNA Met , whereas the only other trypanosomal tRNA Met , the eukaryotic initiator, is found exclusively in the cytosol. Unlike their cytosolic counterparts, organellar initiator tRNAs Met carry a formylated methionine. This raises the question of how initiation of translation works in trypanosomal mitochondria, where only elongator tRNA Met is found. Using in organello charging and formylation assays, we show that unexpectedly a fraction of elongator tRNA Met becomes formylated after import into mitochondria. Furthermore, in vitro experiments with mitochondrial extracts demonstrate that only the trypanosomal elongator and not the initiator tRNA Met is recognized by the formylation activity. Finally, RNA interference assays identify the gene encoding the trypanosomal formylase activity. Whereas the predicted protein is homologous to prokaryotic and mitochondrial methionyl-tRNA Met formyltransferases, it has about twice the mass of any of these proteins. mitochondrial translation ͉ initiator tRNA Met ͉ formylation ͉ mitochondrial tRNA import ͉ methionyl-tRNA Met formyltransferase

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“…After translocation to the outer surface of the inner membrane, ArnT (Orf5, PmrK, or YfbI) transfers the L-Ara4N unit to lipid A (27). The ArnA protein has a second catalytic domain with strong similarity to methionyl-tRNA formyltransferase (34). This may account for the efficient transfer of a formyl group from N-10-formyltetrahydrofolate to UDP-L-Ara4N in our in vitro system (see below), but the significance of this modification is unclear.…”

Section: Fig 2 Biosynthesis Of Udp-l-ara4n From Udp-glca In Polymyxmentioning

confidence: 99%

“…ArnA, which is predicted based upon its sequence to catalyze the NAD-dependent conversion of UDP-GlcA to 1, possesses an additional N-terminal domain of unknown function that displays significant similarity to methionyl-tRNA formyltransferases (34). Given this peculiar observation, we investigated the possibility of a formyltransferase that acts on [␣-…”

Section: Formylation Of [␣-32 P]udp-l-ara4n In Extracts Of Wd101-mentioning

confidence: 99%

“…ArnA is unique, however, in releasing the 4Љ ketone and the NADH products without reutilizing the latter for a subsequent reduction step. ArnA, furthermore, contains a second catalytic domain that is highly homologous to methionyl-tRNA formyltransferase (34). Although the function of the formyltransferase domain of ArnA remains unclear, it is responsible for the UDP-L-Ara4N formylation observed in vitro (Fig.…”

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confidence: 99%

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Oxidative Decarboxylation of UDP-Glucuronic Acid in Extracts of Polymyxin-resistant Escherichia coli

Breazeale¹,

Ribeiro²,

Raetz³

2002

Journal of Biological Chemistry

102

148

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Addition of the 4-amino-4-deoxy-L-arabinose (L-Ara4NPmrI (renamed ArnA) was overexpressed using a T7 construct, and shown by itself to catalyze the unprecedented oxidative decarboxylation of UDP-glucuronic acid to form uridine 5-(␤-L-threo-pentapyranosyl-4؆-ulose diphosphate). A 6-mg sample of the latter was purified, and its structure was validated by NMR studies as the hydrate of the 4؆ ketone. ArnA resembles UDP-galactose epimerase, dTDP-glucose-4,6-dehydratase, and UDP-xylose synthase in oxidizing the C-4؆ position of its substrate, but differs in that it releases the NADH product.

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Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet

Cited by 135 publications

References 36 publications

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

Eukaryotic-type elongator tRNA ^Met of Trypanosoma brucei becomes formylated after import into mitochondria

Oxidative Decarboxylation of UDP-Glucuronic Acid in Extracts of Polymyxin-resistant Escherichia coli

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Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet

Cited by 135 publications

References 36 publications

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

Eukaryotic-type elongator tRNA Met of Trypanosoma brucei becomes formylated after import into mitochondria

Oxidative Decarboxylation of UDP-Glucuronic Acid in Extracts of Polymyxin-resistant Escherichia coli

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Eukaryotic-type elongator tRNA ^Met of Trypanosoma brucei becomes formylated after import into mitochondria