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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.
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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]

    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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