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    rppH RNA pyrophosphohydrolase [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947300, updated on 3-Dec-2024

    Summary

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    Official Symbol
    rppH
    Official Full Name
    RNA pyrophosphohydrolase
    Primary source
    ECOCYC:G7459
    Locus tag
    b2830
    See related
    ASAP:ABE-0009276
    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
    ECK2826; nudH; ygdP
    Summary
    Nudix hydrolase. [More information is available at EcoGene: EG13091]. Mutations disrupting YgdP suppress the temperature-sensitivity of degP null mutants and mirror the effects of mutation in PrlF . [More information is available at EcoCyc: G7459].
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    Genomic context

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    Sequence:
    NC_000913.3 (2968447..2968977, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene phosphatidylglycerol--prolipoprotein diacylglyceryl transferase Neighboring gene phosphoenolpyruvate-protein phosphotransferase PtsP Neighboring gene YgdT Neighboring gene DNA mismatch repair protein MutH

    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. Null mutations in a Nudix gene, ygdP, implicate an alarmone response in a novel suppression of hybrid jamming. Hand NJ, et al. J Bacteriol, 2003 Nov. PMID 14594825, Free PMC Article
    2. Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH. Gao A, et al. Nucleic Acids Res, 2020 Apr 17. PMID 31960065, Free PMC Article
    3. The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Deana A, et al. Nature, 2008 Jan 17. PMID 18202662
    4. 1H, 13C and 15N resonance assignments of RNA pyrophosphohydrolase RppH from Escherichia coli. Bi Y, et al. Biomol NMR Assign, 2009 Jun. PMID 19636968
    5. The gene ygdP, associated with the invasiveness of Escherichia coli K1, designates a Nudix hydrolase, Orf176, active on adenosine (5')-pentaphospho-(5')-adenosine (Ap5A). Bessman MJ, et al. J Biol Chem, 2001 Oct 12. PMID 11479323

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. E. coli RppH integrates various signals, such as competing non-cognate substrates and a stimulatory protein factor DapF, to achieve the differential degradation of transcripts.
      Title: Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
    2. Structural studies show that DapF potentiates RppH dependent RNA degradation in two ways.
      Title: Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.
    3. it was also determined that diphosphorylated mRNA decay intermediates are abundant in wild-type E. coli and that their fractional level increases to almost 100% for representative mRNAs in mutant cells lacking RppH.
      Title: Importance of a diphosphorylated intermediate for RppH-dependent RNA degradation.
    4. The authors propose that in both Azotobacter vinelandii and Escherichia coli, RppH activity plays a role in the expression of the translational regulator protein RsmA/CsrA.
      Title: The pyrophosphohydrolase RppH is involved in the control of RsmA/CsrA expression in Azotobacter vinelandii and Escherichia coli.
    5. study examined phenotypes of the rppH mutant strain to define the physiological role of RppH in more detail; through various phenotypic analyses of the rppH mutant, found the rppH mutant cells have increased envelope permeability; propose that RppH is associated with regulation of envelope integrity
      Title: Effect of the RNA pyrophosphohydrolase RppH on envelope integrity in Escherichia coli.
    6. Triphosphate-to-monophosphate conversion to induce 5' end-dependent RNA degradation is a two-step process in E. coli involving gamma-phosphate removal by an unidentified enzyme to enable subsequent beta-phosphate removal by RppH.
      Title: A Novel RNA Phosphorylation State Enables 5' End-Dependent Degradation in Escherichia coli.
    7. Data indicate that X-ray structures of RNA pyrophosphohydrolase RppH have revealed molecular features important for RNA recognition.
      Title: Structures of RNA complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5'-end-dependent mRNA decay.
    8. Data show that the specificity of RNA pyrophosphohydrolase RppH is species-dependent.
      Title: Specificity and evolutionary conservation of the Escherichia coli RNA pyrophosphohydrolase RppH.
    9. The data suggest that the cellular level of DapF is a critical factor regulating the RppH-catalyzed pyrophosphate removal and the subsequent degradation of target mRNAs.
      Title: RppH-dependent pyrophosphohydrolysis of mRNAs is regulated by direct interaction with DapF in Escherichia coli.
    10. RppH not only catalyses a process functionally reminiscent of eukaryotic mRNA decapping but also bears an evolutionary relationship to the eukaryotic decapping enzyme Dcp2
      Title: The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal.
    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 RNA NAD-cap (NMN-forming) hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA 5'-diphosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA 5'-diphosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pyrophosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in NAD-cap decapping IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA decapping IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA decapping IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in RNA destabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RNA pyrophosphohydrolase

    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
      2968447..2968977 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417307.1 RNA pyrophosphohydrolase [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417307.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8S0FMR9
      Conserved Domains (1) summary
      PRK00714
      Location:1 → 156
      PRK00714; RNA pyrophosphohydrolase; Reviewed
    Nucleotide Protein
    Heading Accession and Version

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