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    rlmH 23S rRNA m(3)psi1915 methyltransferase [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 945239, updated on 3-Dec-2024

    Summary

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    Official Symbol
    rlmH
    Official Full Name
    23S rRNA m(3)psi1915 methyltransferase
    Primary source
    ECOCYC:EG11254
    Locus tag
    b0636
    See related
    ASAP:ABE-0002180
    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
    ECK0629; ybeA
    Summary
    AFMB Structural Genomics target Number 125 (http://afmb.cnrs-mrs.fr/article171.html). [More information is available at EcoGene: EG11254]. RlmH is a methyltransferase that catalyzes the addition of a methyl group in the N3 position of the pseudouridine () residue at nucleotide 1915 in 23S rRNA . [More information is available at EcoCyc: EG11254].
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    Genomic context

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    Sequence:
    NC_000913.3 (668248..668715, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene peptidoglycan glycosyltransferase MrdB Neighboring gene peptidoglycan DD-transpeptidase MrdA Neighboring gene ribosomal silencing factor RsfS Neighboring gene putative adenosylcobalamin phosphatase/alpha-ribazole phosphatase

    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. Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine. Koh CS, et al. Sci Rep, 2017 Apr 20. PMID 28428565, Free PMC Article
    2. Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions. Puri S, et al. Biochem Biophys Res Commun, 2023 Sep 10. PMID 37343318
    3. YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. Purta E, et al. RNA, 2008 Oct. PMID 18755835, Free PMC Article
    4. Experimental detection of knotted conformations in denatured proteins. Mallam AL, et al. Proc Natl Acad Sci U S A, 2010 May 4. PMID 20393125, Free PMC Article
    5. Dodging the crisis of folding proteins with knots. Sułkowska JI, et al. Proc Natl Acad Sci U S A, 2009 Mar 3. PMID 19211785, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions.
      Title: Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions.
    2. Data suggest that E. coli RlmH functions as a dimer, with the S-adenosyl-methionine binding pocket of one monomer and the C-terminal residues of its counterpart forming a composite active site. Study proposes that the C-terminal tail provides a residue that acts as a general base while the other conserved residues form a network of interactions that organize the catalytic site.
      Title: Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine.
    3. While the synthesis of Psis in H69 by RluD is relatively insensitive to the point mutations at neighboring positions, methylation of one of the Psis by RlmH exhibited a much stronger sensitivity.
      Title: Different sensitivity of H69 modification enzymes RluD and RlmH to mutations in Escherichia coli 23S rRNA.
    4. show that RlmH has unique substrate specificity among rRNA modification enzymes
      Title: Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD.
    5. E. coli protein YbeA as the methyltransferase methylating Psi1915 in 23S rRNA was identified.
      Title: Identification of pseudouridine methyltransferase in Escherichia coli.
    6. The identity of the methyltransferase YbeA (redesignated RlmH for rRNA large subunit methyltransferase H) that specifically catalyzes methyl group addition to form m(3)Psi1915 is reported.
      Title: YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
    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 methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein homodimerization activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables rRNA (pseudouridine-N3-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables rRNA (pseudouridine-N3-)-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA (pseudouridine-N3-)-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables ribosome binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA base methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in rRNA methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    23S rRNA m(3)psi1915 methyltransferase
    NP_415169.1

    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
      668248..668715 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_415169.1 23S rRNA m(3)psi1915 methyltransferase [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_415169.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A5B9AX48
      Conserved Domains (1) summary
      TIGR00246
      Location:2 → 154
      tRNA_RlmH_YbeA; rRNA large subunit m3Psi methyltransferase RlmH
    Nucleotide Protein
    Heading Accession and Version

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