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    rluD 23S rRNA pseudouridine(1911/1915/1917) synthase [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947087, updated on 3-Dec-2024

    Summary

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    Official Symbol
    rluD
    Official Full Name
    23S rRNA pseudouridine(1911/1915/1917) synthase
    Primary source
    ECOCYC:EG12098
    Locus tag
    b2594
    See related
    ASAP:ABE-0008532
    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
    ECK2592; sfhB; yfiI
    Summary
    The very poor growth of rluD mutants can be suppressed by a point mutation in prfB and a role in translation termination for the 23S rRNA helix 69 pseudouridines has been demonstrated (Ejby, 2007). [More information is available at EcoGene: EG12098]. RluD is a pseudouridine synthase that catalyzes pseudouridine formation at positions 1911, 1915, and 1917 in helix 69 of the 23S rRNA . [More information is available at EcoCyc: EG12098].
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    Genomic context

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    Sequence:
    NC_000913.3 (2735031..2736011, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene 16S ribosomal RNA Neighboring gene ClpB80;chaperone protein ClpB Neighboring gene ncRNA Neighboring gene purine nucleoside phosphorylase YfiH Neighboring gene outer membrane protein assembly factor BamD Neighboring gene ribosome-associated inhibitor A Neighboring gene ncRNA

    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. Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli. Del Campo M, et al. RNA, 2004 Feb. PMID 14730022, Free PMC Article
    2. Persister cells resuscitate via ribosome modification by 23S rRNA pseudouridine synthase RluD. Song S, et al. Environ Microbiol, 2020 Mar. PMID 31608580
    3. The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli. Gutgsell NS, et al. RNA, 2005 Jul. PMID 15928344, Free PMC Article
    4. Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. Sivaraman J, et al. J Mol Biol, 2004 Jan 2. PMID 14659742
    5. Purification and crystallization of Escherichia coli pseudouridine synthase RluD. Del Campo M, et al. Acta Crystallogr D Biol Crystallogr, 2003 Oct. PMID 14501142

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli.
      Title: An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli.
    2. Persister cells resuscitate via ribosome modification by 23S rRNA pseudouridine synthase RluD.
      Title: Persister cells resuscitate via ribosome modification by 23S rRNA pseudouridine synthase RluD.
    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. Strikingly, tmRNA-mediated SsrA peptide tagging of two proteins, ribosomal protein S7 and LacI, was dramatically increased in DeltarluD cells.
      Title: Deletion of the RluD pseudouridine synthase promotes SsrA peptide tagging of ribosomal protein S7.
    5. RluD is the first rRNA pseudouridine synthase to be kinetically characterized.
      Title: Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD.
    6. RluD directed isomerization of uridines occurs as a late step during the assembly of the large ribosomal subunit.
      Title: Substrate specificity of the pseudouridine synthase RluD in Escherichia coli.
    7. RluD is far more efficient in modifying H69 in structured 50S subunits, compared to free or synthetic 23S rRNA.
      Title: RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA.
    8. N-terminus verified by Edman degradation on mature peptide
      Title: Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD).
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables 23S rRNA pseudouridine(1911/1915/1917) synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables isomerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pseudouridine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pseudouridine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA pseudouridine synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables rRNA pseudouridine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    contributes_to ribosomal small subunit binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in enzyme-directed rRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in enzyme-directed rRNA pseudouridine synthesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in enzyme-directed rRNA pseudouridine synthesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in pseudouridine synthesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ribosomal large subunit assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosome biogenesis 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 pseudouridine(1911/1915/1917) synthase
    NP_417085.1

    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
      2735031..2736011 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417085.1 23S rRNA pseudouridine(1911/1915/1917) synthase [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417085.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8T6QBZ1
      Conserved Domains (1) summary
      PRK11180
      Location:1 → 325
      rluD; 23S rRNA pseudouridine(1911/1915/1917) synthase RluD
    Nucleotide Protein
    Heading Accession and Version

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