Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN

Alexey Silakov, Tyler L. Grove, Matthew I. Radle, Matthew R. Bauerle, Michael T. Green, Amy C. Rosenzweig, Amie Kathleen Boal, Squire J. Booker

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein-nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13 C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl- 13 C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process.

Original languageEnglish (US)
Pages (from-to)8221-8228
Number of pages8
JournalJournal of the American Chemical Society
Volume136
Issue number23
DOIs
StatePublished - Jun 11 2014

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Methylation
Nucleic acids
Nucleic Acids
Proteins
Substrates
Enzymes
Catalysis
Adenosine
Carbon
S-Adenosylmethionine
Electron Spin Resonance Spectroscopy
Methyltransferases
Adenine
Nucleotides
Labeling
Paramagnetic resonance
Catalytic Domain
Spectrum Analysis
Substitution reactions
X-Rays

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Silakov, Alexey ; Grove, Tyler L. ; Radle, Matthew I. ; Bauerle, Matthew R. ; Green, Michael T. ; Rosenzweig, Amy C. ; Boal, Amie Kathleen ; Booker, Squire J. / Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN. In: Journal of the American Chemical Society. 2014 ; Vol. 136, No. 23. pp. 8221-8228.
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title = "Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN",
abstract = "RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein-nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13 C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl- 13 C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process.",
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Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN. / Silakov, Alexey; Grove, Tyler L.; Radle, Matthew I.; Bauerle, Matthew R.; Green, Michael T.; Rosenzweig, Amy C.; Boal, Amie Kathleen; Booker, Squire J.

In: Journal of the American Chemical Society, Vol. 136, No. 23, 11.06.2014, p. 8221-8228.

Research output: Contribution to journalArticle

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T1 - Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN

AU - Silakov, Alexey

AU - Grove, Tyler L.

AU - Radle, Matthew I.

AU - Bauerle, Matthew R.

AU - Green, Michael T.

AU - Rosenzweig, Amy C.

AU - Boal, Amie Kathleen

AU - Booker, Squire J.

PY - 2014/6/11

Y1 - 2014/6/11

N2 - RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein-nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13 C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl- 13 C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process.

AB - RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein-nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13 C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl- 13 C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process.

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