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    rlmN 23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 946249, updated on 3-Dec-2024

    Summary

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    Official Symbol
    rlmN
    Official Full Name
    23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase
    Primary source
    ECOCYC:EG12401
    Locus tag
    b2517
    See related
    ASAP:ABE-0008287
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK2513; yfgB
    Summary
    Radical SAM superfamily. [More information is available at EcoGene: EG12401]. RlmN is the methyltransferase responsible for methylation of 23S rRNA at the C2 position of the A2503 nucleotide . [More information is available at EcoCyc: EG12401].
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    Genomic context

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    Sequence:
    NC_000913.3 (2643129..2644283, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (flavodoxin) Neighboring gene cytoskeleton protein RodZ Neighboring gene nucleoside diphosphate kinase Neighboring gene peptidoglycan glycosyltransferase PbpC

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA. Schwalm EL, et al. Science, 2016 Apr 15. PMID 27081063, Free PMC Article
    2. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. Tsai K, et al. Elife, 2022 Jan 11. PMID 35015630, Free PMC Article
    3. The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. Benítez-Páez A, et al. RNA, 2012 Oct. PMID 22891362, Free PMC Article
    4. Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation. Grove TL, et al. J Am Chem Soc, 2011 Dec 14. PMID 21916495, Free PMC Article
    5. Structural basis for methyl transfer by a radical SAM enzyme. Boal AK, et al. Science, 2011 May 27. PMID 21527678, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.
      Title: Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.
    2. this study reports the x-ray structure of a key intermediate in the RlmN reaction, in which a Cys(118)-->Ala variant of the protein is cross-linked to a tRNA(Glu)substrate through the terminal methylene carbon of a formerly methylcysteinyl residue and C2 of adenosine 37.
      Title: Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA.
    3. RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy.
      Title: The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy.
    4. Reconstitution of the [4Fe-4S] cluster on wild-type apo RlmN followed by addition of S-adenosylmethionine results in rapid production of S-adenosylhomocysteine and the mCys residue.
      Title: Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation.
    5. structure of RlmN and RlmN with SAM show single molecule of SAM coordinates [4Fe-4S] cluster; residue Cys(355) is S-methylated and located proximal to SAM methyl group, suggesting SAM that is involved in the initial methyl transfer binds at the same site
      Title: Structural basis for methyl transfer by a radical SAM enzyme.
    6. SAM enzymes identified that methylate C atoms not inherently nucleophilic via intermediacy of 5'-deoxyadenosyl 5'-radical; determined reaction mechanism targeting sp(2)-hybridized carbons at position 2 and 8 of adenosine in 23S RRNA catalyzed by RlmN, Cfr
      Title: A radically different mechanism for S-adenosylmethionine-dependent methyltransferases.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables 4 iron, 4 sulfur cluster binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 4 iron, 4 sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron-sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rRNA (adenine(2503)-C2-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables rRNA (adenine(2503)-C2-)-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA (adenine(2503)-C2-)-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables rRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables tRNA (adenine(37)-C2)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA (adenine(37)-C2)-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables tRNA (adenine(37)-C2)-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables tRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA base methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rRNA base methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA base methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to antibiotic IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase
    NP_417012.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      2643129..2644283 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417012.1 23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417012.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8S7QY38
      Conserved Domains (1) summary
      PRK11194
      Location:13 → 384
      PRK11194; ribosomal RNA large subunit methyltransferase N; Provisional
    Nucleotide Protein
    Heading Accession and Version

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