U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 947243, updated on 3-Dec-2024

    Summary

    Go to the top of the page Help
    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].
    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 (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

    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. 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

    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 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 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
    		  
    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

    Go to the top of the page Help
    Preferred Names
    23S rRNA m(5)U1939 methyltransferase
    NP_417265.1

    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
      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
    Heading Accession and Version

    Gene LinkOut

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