U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Go to the top of the page Help
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].
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help
Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase
NP_417012.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.