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    dbpA ATP-dependent RNA helicase DbpA [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947153, updated on 3-Dec-2024

    Summary

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    Official Symbol
    dbpA
    Official Full Name
    ATP-dependent RNA helicase DbpA
    Primary source
    ECOCYC:EG10210
    Locus tag
    b1343
    See related
    ASAP:ABE-0004511
    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
    ECK1340; rhlC
    Summary
    DbpA is a 3'->5' RNA helicase that is thought to play a role in biogenesis of the 50S subunit of the ribosome . [More information is available at EcoCyc: EG10210].
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    Genomic context

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    Sequence:
    NC_000913.3 (1409511..1410884)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene protein YnaL Neighboring gene tRNA cytosine(32) 2-sulfurtransferase TtcA Neighboring gene putative integrase

    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. A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Sharpe Elles LM, et al. Nucleic Acids Res, 2009 Oct. PMID 19734347, Free PMC Article
    2. Identification of a putative RNA helicase in E.coli. Iggo R, et al. Nucleic Acids Res, 1990 Sep 25. PMID 2216714, Free PMC Article
    3. Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy. Henn A, et al. Proc Natl Acad Sci U S A, 2001 Apr 24. PMID 11296244, Free PMC Article
    4. The RNA helicase DbpA exhibits a markedly different conformation in the ADP-bound state when compared with the ATP- or RNA-bound states. Henn A, et al. J Biol Chem, 2002 Nov 29. PMID 12324462
    5. Interaction of Escherichia coli DbpA with 23S rRNA in different functional states of the enzyme. Karginov FV, et al. Nucleic Acids Res, 2004. PMID 15173385, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.
      Title: Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.
    2. Overexpression of the inactive DbpA R331A mutant appears to block assembly at a late stage when the peptidyl transferase center is formed, indicating a possible role for DbpA promoting this conformational change.
      Title: A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit.
    3. The presented analysis of the DbpA ATPase cycle reaction mechanism provides a rigorous kinetic and thermodynamic foundation for developing testable hypotheses regarding the functions and molecular mechanisms of DEAD-box helicases.
      Title: The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA.
    4. Identification of dominant-negative mutant form of DbpA that results in a slow growth phenotype.
      Title: Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype.
    5. ADP binding increases the conformational flexibility and dynamics of DbpA
      Title: Equilibrium and kinetic analysis of nucleotide binding to the DEAD-box RNA helicase DbpA.
    6. The directionality of helicase activity of DbpA has been determined; DbpA is defined as a 3'-> 5' helicase.
      Title: Escherichia coli DbpA is a 3' --> 5' RNA helicase.
    7. results favor models where DbpA functions as an active monomer that possesses two distinct RNA binding sites, one in the helicase core domain and the other in the carboxyl-terminal domain
      Title: Hydrodynamic characterization of the DEAD-box RNA helicase DbpA.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables 3'-5' RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 3'-5' RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ADP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA/RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ribosomal large subunit assembly 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
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase DbpA

    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
      1409511..1410884
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_415859.1 ATP-dependent RNA helicase DbpA [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_415859.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8S7RGG9
      Conserved Domains (1) summary
      PRK11776
      Location:1 → 457
      PRK11776; ATP-dependent RNA helicase DbpA; Provisional
    Nucleotide Protein
    Heading Accession and Version

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