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rlmD 23S rRNA m(5)U1939 methyltransferase [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 947243, updated on 26-Mar-2025

Summary

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Official Symbol
rlmD
Official Full Name
23S rRNA m(5)U1939 methyltransferase
Primary source
ECOCYC:EG11247
Locus tag
b2785
See related
ASAP:ABE-0009127
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
ECK2779; rumA; ygcA
Summary
Although this purified proten had its N-terminus sequenced (reported in Medline 21883956, Agarwalla et al.) it is not included in the Verified set since translation was forced at the predicted start codon. [More information is available at EcoGene: EG11247]. RlmD is the methyltransferase responsible for methylation of 23S rRNA at the C5 position of the U1939 nucleotide . [More information is available at EcoCyc: EG11247].
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Genomic context

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Sequence:
NC_000913.3 (2913699..2915000, complement)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene endoribonuclease toxin MazF Neighboring gene antitoxin of the MazF-MazE toxin-antitoxin system MazE Neighboring gene GDP/GTP pyrophosphokinase Neighboring gene sensor histidine kinase BarA Neighboring gene D-glucarate dehydratase

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. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Purta E, et al. Mol Microbiol, 2009 Jun. PMID 19400805
  2. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Lee TT, et al. Cell, 2005 Mar 11. PMID 15766524
  3. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. Agarwalla S, et al. J Biol Chem, 2004 Aug 13. PMID 15181002, Free PMC Article
  4. Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Lee TT, et al. Structure, 2004 Mar. PMID 15016356
  5. Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective. Hur S, et al. J Biol Chem, 2006 Dec 22. PMID 17085441

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era.
    Title: A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
Submit: New GeneRIF Correction

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 binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables S-adenosylmethionine-dependent methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables iron ion binding 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 rRNA (uridine-C5-)-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables rRNA (uridine-C5-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables rRNA (uridine-C5-)-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA modification IEA
Inferred from Electronic Annotation
more info
  
involved_in RNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in rRNA base methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within rRNA base methylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rRNA methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in rRNA processing IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
23S rRNA m(5)U1939 methyltransferase
NP_417265.1

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
    2913699..2915000 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_417265.1 23S rRNA m(5)U1939 methyltransferase [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_417265.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A831GGS0
    Conserved Domains (1) summary
    PRK13168
    Location:2 → 431
    rumA; 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
Nucleotide Protein
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