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deoD purine nucleoside phosphorylase [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 945654, updated on 2-May-2024

Summary

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Gene symbol
deoD
Gene description
purine nucleoside phosphorylase
Primary source
ASAP:ABE-0014379
Locus tag
b4384
See related
ECOCYC:EG10222
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
ECK4376; pup
Summary
DeoD has reversible purine nucleoside phosphorylase (PNP) activity with broad substrate specificity; however, it does not act on xanthosine or pyrimidine nucleosides . [More information is available at EcoCyc: EG10222].
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Genomic context

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Sequence:
NC_000913.3 (4620883..4621602)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene thymidine phosphorylase Neighboring gene phosphopentomutase Neighboring gene toxin YjjJ Neighboring gene lipoate--protein ligase A

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. Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis. Štefanić Z, et al. Sci Rep, 2018 Oct 18. PMID 30337572, Free PMC Article
  2. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A. Sobieraj M, et al. J Mol Model, 2015 Apr. PMID 25754135, Free PMC Article
  3. Homooligomerization is needed for stability: a molecular modelling and solution study of Escherichia coli purine nucleoside phosphorylase. Bertoša B, et al. FEBS J, 2014 Apr. PMID 24785777
  4. New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A. Štefanić Z, et al. FEBS Lett, 2012 Apr 5. PMID 22569248
  5. Cloning and characterization of purine nucleoside phosphorylase in Escherichia coli and subsequent ribavirin biosynthesis using immobilized recombinant cells. Luo W, et al. Enzyme Microb Technol, 2011 May 6. PMID 22113014

See all (64) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wild-type purine nucleoside phosphorylase, which does not exist in the Ala159 mutant, and for the effective association of PNP with formycin A .
    Title: A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A.
  2. Data suggest that in active sites of purine nucleoside phosphorylase complexed with phosphate and formycin A, recombinant enzyme exhibits unexpected binding site for phosphate and exhibits stoichiometry of two phosphate molecules per enzyme subunit.
    Title: New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A.
  3. The deoD gene was cloned from Escherichia coli MG1665 & overexpressed in E. coli BL 21(DE3).
    Title: Cloning and characterization of purine nucleoside phosphorylase in Escherichia coli and subsequent ribavirin biosynthesis using immobilized recombinant cells.
  4. Role of ionization of the phosphate cosubstrate on phosphorolysis by purine nucleoside phosphorylase (PNP)
    Title: Role of ionization of the phosphate cosubstrate on phosphorolysis by purine nucleoside phosphorylase (PNP) of bacterial (E. coli) and mammalian (human) origin.
  5. N-terminus verified by Edman degradation on mature peptide
    Title: The biosynthesis of molybdopterin in Escherichia coli. Purification and characterization of the converting factor.
  6. in solution similar to the crystal, E. coli PNP is a hexameric molecule and previous suggestions for coexistence of two oligomeric forms are incorrect.
    Title: Molecular architecture of E. coli purine nucleoside phosphorylase studied by analytical ultracentrifugation and CD spectroscopy.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables glycosyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables guanosine phosphorylase activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables purine-nucleoside phosphorylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables purine-nucleoside phosphorylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables purine-nucleoside phosphorylase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in nucleoside catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleoside metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in purine nucleoside catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within purine nucleoside catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within purine nucleoside interconversion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in purine nucleoside metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol HDA PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 

General protein information

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Preferred Names
purine nucleoside phosphorylase
NP_418801.1

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
    4620883..4621602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_418801.1 purine nucleoside phosphorylase [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_418801.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A418GHN3
    Conserved Domains (1) summary
    PRK05819
    Location:2 → 236
    deoD; DeoD-type purine-nucleoside phosphorylase
Nucleotide Protein
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Other Literature Sources
Molecular Biology Databases
Research Materials