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pdeF cyclic di-GMP phosphodiesterase PdeF [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 946968, updated on 3-Dec-2024

Summary

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Official Symbol
pdeF
Official Full Name
cyclic di-GMP phosphodiesterase PdeF
Primary source
ECOCYC:G7314
Locus tag
b2503
See related
ASAP:ABE-0008240
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
ECK2499; yfgF
Summary
YfgF has a central GGDEF putative diguanylate cyclase, then a C-terminal putative cyclic-di-GMP phosphodiesterase EAL domain. [More information is available at EcoGene: EG14202]. YfgF is an inner membrane protein with nine predicted transmembrane domains. [More information is available at EcoCyc: G7314].
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Genomic context

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Sequence:
NC_000913.3 (2626695..2628938, complement)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene polyphosphate kinase Neighboring gene exopolyphosphatase Neighboring gene nickel/cobalt stress response protein YfgG Neighboring gene lipoprotein YfgH

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. Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase with roles in cell surface remodelling and the oxidative stress response. Lacey MM, et al. Microbiology (Reading), 2010 Sep. PMID 20522491
  2. The Escherichia coli yhjA gene, encoding a predicted cytochrome c peroxidase, is regulated by FNR and OxyR. Partridge JD, et al. Microbiology (Reading), 2007 May. PMID 17464064
  3. A comprehensive genetic characterization of bacterial motility. Girgis HS, et al. PLoS Genet, 2007 Sep. PMID 17941710, Free PMC Article
  4. C-di-GMP: the dawning of a novel bacterial signalling system. Römling U, et al. Mol Microbiol, 2005 Aug. PMID 16045609
  5. Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli. Sommerfeldt N, et al. Microbiology (Reading), 2009 Apr. PMID 19332833

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. YfgF is involved in cell surface remodelling and the oxidative stress response.
    Title: Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase with roles in cell surface remodelling and the oxidative stress response.
Submit: New GeneRIF Correction

General gene information

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Homology

Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables cyclic-guanylate-specific phosphodiesterase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables cyclic-guanylate-specific phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cellular response to anoxia IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cellular response to hydrogen peroxide IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of single-species biofilm formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
cyclic di-GMP phosphodiesterase PdeF
NP_416998.1

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
    2626695..2628938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_416998.1 cyclic di-GMP phosphodiesterase PdeF [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_416998.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A377DNJ9
    Conserved Domains (3) summary
    smart00267
    Location:328 → 480
    GGDEF; diguanylate cyclase
    smart00052
    Location:497 → 735
    EAL; Putative diguanylate phosphodiesterase
    pfam05231
    Location:15 → 320
    MASE1
Nucleotide Protein
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