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Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA

Wang, Kai-Tuo ; Desmolaize, Benoit ; Nan, Jie LU ; Zhang, Xiao-Wei LU ; Li, Lan-Fen ; Douthwaite, Stephen and Su, Xiao-Dong LU (2012) In Nucleic Acids Research 40(11). p.48-5138
Abstract

The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445... (More)

The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.

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author
; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
keywords
Catalytic Domain, Escherichia coli, Escherichia coli Proteins, Evolution, Molecular, Methyltransferases, Models, Molecular, RNA, Ribosomal, 23S, Streptococcus mutans
in
Nucleic Acids Research
volume
40
issue
11
pages
11 pages
publisher
Oxford University Press
external identifiers
  • pmid:22362734
  • scopus:84862156291
ISSN
1362-4962
DOI
10.1093/nar/gks160
language
English
LU publication?
yes
id
24ff8146-da52-4f7c-9eb4-d4f4658112a6
date added to LUP
2016-09-07 22:51:17
date last changed
2024-04-05 04:24:08
@article{24ff8146-da52-4f7c-9eb4-d4f4658112a6,
  abstract     = {{<p>The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.</p>}},
  author       = {{Wang, Kai-Tuo and Desmolaize, Benoit and Nan, Jie and Zhang, Xiao-Wei and Li, Lan-Fen and Douthwaite, Stephen and Su, Xiao-Dong}},
  issn         = {{1362-4962}},
  keywords     = {{Catalytic Domain; Escherichia coli; Escherichia coli Proteins; Evolution, Molecular; Methyltransferases; Models, Molecular; RNA, Ribosomal, 23S; Streptococcus mutans}},
  language     = {{eng}},
  number       = {{11}},
  pages        = {{48--5138}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA}},
  url          = {{http://dx.doi.org/10.1093/nar/gks160}},
  doi          = {{10.1093/nar/gks160}},
  volume       = {{40}},
  year         = {{2012}},
}