Post-translational modification of ribosomal proteins: Structural and functional characterization of RimO from thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase

Simon Arragain, Ricardo Garcia-Serres, Geneviève Blondin, Thierry Douki, Martin Clemancey, Jean Marc Latour, Farhad Forouhar, Helen Neely, Gaetano Montelione, John F. Hunt, Etienne Mulliez, Marc Fontecave, Mohamed Atta

Research output: Contribution to journalArticle

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Abstract

Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs.Wepresent spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0Å crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.

Original languageEnglish (US)
Pages (from-to)5792-5801
Number of pages10
JournalJournal of Biological Chemistry
Volume285
Issue number8
DOIs
StatePublished - Feb 19 2010

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Thermotoga maritima
Triose-Phosphate Isomerase
S-Adenosylmethionine
Ribosomal Proteins
Post Translational Protein Processing
Cysteine
tRNA Methyltransferases
Derivatives
Anticodon
Enzymes
Transfer RNA
Aspartic Acid
Adenosine
Machinery
Decoding
Proteins
Genes
Crystal structure
Peptides
Substrates

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Arragain, Simon ; Garcia-Serres, Ricardo ; Blondin, Geneviève ; Douki, Thierry ; Clemancey, Martin ; Latour, Jean Marc ; Forouhar, Farhad ; Neely, Helen ; Montelione, Gaetano ; Hunt, John F. ; Mulliez, Etienne ; Fontecave, Marc ; Atta, Mohamed. / Post-translational modification of ribosomal proteins : Structural and functional characterization of RimO from thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. In: Journal of Biological Chemistry. 2010 ; Vol. 285, No. 8. pp. 5792-5801.
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abstract = "Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs.Wepresent spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0{\AA} crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.",
author = "Simon Arragain and Ricardo Garcia-Serres and Genevi{\`e}ve Blondin and Thierry Douki and Martin Clemancey and Latour, {Jean Marc} and Farhad Forouhar and Helen Neely and Gaetano Montelione and Hunt, {John F.} and Etienne Mulliez and Marc Fontecave and Mohamed Atta",
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Arragain, S, Garcia-Serres, R, Blondin, G, Douki, T, Clemancey, M, Latour, JM, Forouhar, F, Neely, H, Montelione, G, Hunt, JF, Mulliez, E, Fontecave, M & Atta, M 2010, 'Post-translational modification of ribosomal proteins: Structural and functional characterization of RimO from thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase', Journal of Biological Chemistry, vol. 285, no. 8, pp. 5792-5801. https://doi.org/10.1074/jbc.M109.065516

Post-translational modification of ribosomal proteins : Structural and functional characterization of RimO from thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. / Arragain, Simon; Garcia-Serres, Ricardo; Blondin, Geneviève; Douki, Thierry; Clemancey, Martin; Latour, Jean Marc; Forouhar, Farhad; Neely, Helen; Montelione, Gaetano; Hunt, John F.; Mulliez, Etienne; Fontecave, Marc; Atta, Mohamed.

In: Journal of Biological Chemistry, Vol. 285, No. 8, 19.02.2010, p. 5792-5801.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Post-translational modification of ribosomal proteins

T2 - Structural and functional characterization of RimO from thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase

AU - Arragain, Simon

AU - Garcia-Serres, Ricardo

AU - Blondin, Geneviève

AU - Douki, Thierry

AU - Clemancey, Martin

AU - Latour, Jean Marc

AU - Forouhar, Farhad

AU - Neely, Helen

AU - Montelione, Gaetano

AU - Hunt, John F.

AU - Mulliez, Etienne

AU - Fontecave, Marc

AU - Atta, Mohamed

PY - 2010/2/19

Y1 - 2010/2/19

N2 - Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs.Wepresent spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0Å crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.

AB - Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs.Wepresent spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0Å crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.

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