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Information on EC 2.1.1.192 - 23S rRNA (adenine2503-C2)-methyltransferase and Organism(s) Escherichia coli and UniProt Accession P36979

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IUBMB Comments
Contains an [4Fe-4S] cluster . This enzyme is a member of the 'AdoMet radical' (radical SAM) family. S-Adenosyl-L-methionine acts as both a radical generator and as the source of the appended methyl group. RlmN first transfers an CH2 group to a conserved cysteine (Cys355 in Escherichia coli) , the generated radical from a second S-adenosyl-L-methionine then attacks the methyl group, exctracting a hydrogen. The formed radical forms a covalent intermediate with the adenine group of the tRNA . RlmN is an endogenous enzyme used by the cell to refine functions of the ribosome in protein synthesis . The enzyme methylates adenosine by a radical mechanism with CH2 from the S-adenosyl-L-methionine and retention of the hydrogen at C-2 of adenosine2503 of 23S rRNA. It will also methylate 8-methyladenosine2503 of 23S rRNA. cf. EC 2.1.1.224 [23S rRNA (adenine2503-C8)-methyltransferase].
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Escherichia coli
UNIPROT: P36979
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The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
radical s-adenosyl-l-methionine enzyme, rlmn methyltransferase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
methyltransferase YfgB/RlmN
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radical S-adenosyl-L-methionine enzyme
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radical SAM enzyme
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RlmN methyltransferase
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YfgB/RlmN
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:23S rRNA (adenine2503-C2)-methyltransferase
Contains an [4Fe-4S] cluster [2]. This enzyme is a member of the 'AdoMet radical' (radical SAM) family. S-Adenosyl-L-methionine acts as both a radical generator and as the source of the appended methyl group. RlmN first transfers an CH2 group to a conserved cysteine (Cys355 in Escherichia coli) [6], the generated radical from a second S-adenosyl-L-methionine then attacks the methyl group, exctracting a hydrogen. The formed radical forms a covalent intermediate with the adenine group of the tRNA [9]. RlmN is an endogenous enzyme used by the cell to refine functions of the ribosome in protein synthesis [2]. The enzyme methylates adenosine by a radical mechanism with CH2 from the S-adenosyl-L-methionine and retention of the hydrogen at C-2 of adenosine2503 of 23S rRNA. It will also methylate 8-methyladenosine2503 of 23S rRNA. cf. EC 2.1.1.224 [23S rRNA (adenine2503-C8)-methyltransferase].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA
S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA
show the reaction diagram
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
-
-
-
?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
-
-
-
?
2 S-adenosyl-L-methionine + adenine37 in tRNA + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNA + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
-
-
-
?
2 S-adenosyl-L-methionine + adenine37 in tRNAArg(ACG) + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNAArg(ACG) + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
low activity with tRNAArg(ACG)
-
-
?
2 S-adenosyl-L-methionine + adenine37 in tRNAAsp(GUC) + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNAAsp(GUC) + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
very low activity with tRNAAsp(GUC)
-
-
?
2 S-adenosyl-L-methionine + adenine37 in tRNAGln(CUG) + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNAGln(CUG) + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
moderate activity with tRNAGln(CUG)
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-
?
2 S-adenosyl-L-methionine + adenine37 in tRNAGln(UUG) + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNAGln(UUG) + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
high activity with tRNAGln(UUG)
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-
?
2 S-adenosyl-L-methionine + adenine37 in tRNAGlu(UUC) + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNAGlu(UUC) + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
low activity with tRNAGlu(UUC)
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-
?
2 S-adenosyl-L-methionine + adenine37 in tRNAHis(GUG) + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNAHis(GUG) + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
best tRNA substrate
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-
?
S-adenosyl-L-methionine + adenine2503 in 23S rRNA
S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA
S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA
show the reaction diagram
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
-
-
-
?
2 S-adenosyl-L-methionine + adenine37 in tRNA + 2 reduced [2Fe-2S] ferredoxin
2 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNA + 2 oxidized [2Fe-2S] ferredoxin
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + adenine2503 in 23S rRNA
S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA
show the reaction diagram
additional information
?
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-
RlmN introduces m2A at position 2503 in the peptidyl transferase center of 23S RNA. RlmN is a dual-specificity enzyme that catalyzes methylation of both rRNA and tRNA, see for EC 2.1.1.66, substrate specificity analysis, overview
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4Fe-4S-center
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reduced [2Fe-2S] ferredoxin
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S-adenosyl-L-methionine
[4Fe-4S] cluster
[4Fe-4S]-center
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-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
physiological function
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
C118A enzyme mutant complexed with tRNAGlu substrate, X-ray diffraction structure determination and analysis at 2.4 A resolution, structure modelling
homology modeling of structure and comparison with Cfr from Staphylococcus sciuri, EC 2.1.1.194
mutant C118A, hanging drop vapor diffusion method, using 7.5% (w/v) PEG 6000, 0.1 M HEPES, pH 7.5, and 5% (v/v) 2-methyl-2,4-pentanediol as the precipitant
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structure of a key intermediate in the RlmN reaction, in which a Cys118Ala variant of the protein is crosslinked to a tRNAGlu substrate through the terminal methylene carbon of a formerly methylcysteinyl residue and C2 of A37. RlmN contacts the entire length of tRNAGlu, accessing A37 using an induced-fit strategy that completely unfolds the tRNA anticodon stem loop
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C118A
C118S
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inactive
E105A
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the mutant shows wild type activity
additional information
construction of chimera between Cfr from Staphylococcus sciuri and RlmN to analyze C2/C8 and C2 methylation specificity, respectively. The catalytic site is expected to be responsible for the C2/C8 specificity of Cfr. Almost all replacements show no function in the primer extension assay, apart from a few that have a weak effect
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant tagged enzyme from Escherichia coli by metal chelating affinity chromatography, anion exchange chromatography, and ultrafiltration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene rlmN, recombinant expression of tagged enzyme in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Toh, S.M.; Xiong, L.; Bae, T.; Mankin, A.S.
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA
RNA
14
98-106
2008
Escherichia coli
Manually annotated by BRENDA team
Benitez-Paez, A.; Villarroya, M.; Armengod, M.E.
The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy
RNA
18
1783-1795
2012
Escherichia coli
Manually annotated by BRENDA team
Atkinson, G.C.; Hansen, L.H.; Tenson, T.; Rasmussen, A.; Kirpekar, F.; Vester, B.
Distinction between the Cfr methyltransferase conferring antibiotic resistance and the housekeeping RlmN methyltransferase
Antimicrob. Agents Chemother.
57
4019-4026
2013
Bacillus subtilis (O34617), Bacillus subtilis 168 (O34617), Escherichia coli, Mammaliicoccus sciuri (Q9FBG4), Thermus thermophilus (Q5SGZ3), Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q5SGZ3)
Manually annotated by BRENDA team
Silakov, A.; Grove, T.L.; Radle, M.I.; Bauerle, M.R.; Green, M.T.; Rosenzweig, A.C.; Boal, A.K.; Booker, S.J.
Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN
J. Am. Chem. Soc.
136
8221-8228
2014
Escherichia coli
Manually annotated by BRENDA team
Ntokou, E.; Hansen, L.; Kongsted, J.; Vester, B.
Biochemical and computational analysis of the substrate specificities of Cfr and RlmN Methyltransferases
PLoS ONE
10
e0145655
2015
Escherichia coli (P36979), Mammaliicoccus sciuri (A0A1X0U0N1)
Manually annotated by BRENDA team
Fitzsimmons, C.M.; Fujimori, D.G.
Determinants of tRNA recognition by the radical SAM enzyme RlmN
PLoS ONE
11
e0167298
2016
Escherichia coli, Escherichia coli (P36979)
Manually annotated by BRENDA team
Benitez-Paez, A.; Villarroya, M.; Armengod, M.-A.
The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy
RNA
18
1783-1795
2012
Escherichia coli (P36979), Escherichia coli
Manually annotated by BRENDA team
Boal, A.K.; Grove, T.L.; McLaughlin, M.I.; Yennawar, N.H.; Booker, S.J.; Rosenzweig, A.C.
Structural basis for methyl transfer by a radical SAM enzyme
Science
332
1089-1092
2011
Escherichia coli (P36979)
Manually annotated by BRENDA team
Schwalm, E.; Grove, T.; Booker, S.; Boal, A.
Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA
Science
352
309-312
2016
Escherichia coli (P36979)
Manually annotated by BRENDA team