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    deaD ATP-dependent RNA helicase DeaD [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947674, updated on 3-Dec-2024

    Summary

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    Official Symbol
    deaD
    Official Full Name
    ATP-dependent RNA helicase DeaD
    Primary source
    ECOCYC:EG10215
    Locus tag
    b3162
    See related
    ASAP:ABE-0010392
    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
    csdA; ECK3150; mssB; rhlD
    Summary
    Mechanism of DeaD 50S biogenesis differs from that for SrmB 50S biogenesis. stabilizes exposed mRNA, possibly by protecting or destabilizing secondary structure of RNase E sites. [More information is available at EcoGene: EG10215]. The CsdA protein participates in the assembly of the large subunit of the ribosome . [More information is available at EcoCyc: EG10215].
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    Genomic context

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    Sequence:
    NC_000913.3 (3305971..3307860, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene putative luciferase-like monooxygenase YhbW Neighboring gene tryptophan:H(+) symporter Mtr Neighboring gene uncharacterized protein YrbN Neighboring gene lipoprotein NlpI Neighboring gene polynucleotide phosphorylase

    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. Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions. Xu L, et al. Structure, 2017 Dec 5. PMID 29107486
    2. Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures. Vakulskas CA, et al. Mol Microbiol, 2014 Jun. PMID 24708042, Free PMC Article
    3. Molecular characterization of a prokaryotic translation factor homologous to the eukaryotic initiation factor eIF4A. Lu J, et al. Int J Biochem Cell Biol, 1999 Jan. PMID 10216955
    4. Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA. Stampfl S, et al. RNA Biol, 2013 Jan. PMID 23291905, Free PMC Article
    5. Functional and molecular analysis of Escherichia coli strains lacking multiple DEAD-box helicases. Jagessar KL, et al. RNA, 2010 Jul. PMID 20484467, Free PMC Article

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Interacts with RNase E
      Title: Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'.
    2. N-terminus verified by Edman degradation on mature peptide
      Title: Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli.
    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 ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 RNA strand annealing activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA strand annealing activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 hydrolase activity, acting on acid anhydrides 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 
    Process Evidence Code Pubs
    involved_in RNA catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within RNA catabolic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in cellular response to cold IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cellular response to cold IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within cellular response to cold IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to cold IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to radiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosomal large subunit assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within ribosomal large subunit assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with ribosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase DeaD

    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
      3305971..3307860 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417631.2 ATP-dependent RNA helicase DeaD [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417631.2

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A5B9AS65, A0A5D8MVY1, A0A792HRV4
      Conserved Domains (1) summary
      PRK11634
      Location:1 → 629
      PRK11634; ATP-dependent RNA helicase DeaD; Provisional
    Nucleotide Protein
    Heading Accession and Version

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