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nrdF ribonucleoside-diphosphate reductase 2 subunit beta [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 947149, updated on 17-Dec-2024

Summary

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Official Symbol
nrdF
Official Full Name
ribonucleoside-diphosphate reductase 2 subunit beta
Primary source
ECOCYC:EG12381
Locus tag
b2676
See related
ASAP:ABE-0008808
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
ECK2670; ygaD
Summary
nrdF is a nonessential gene. [More information is available at EcoGene: EG12381]. Expression of the nrdHIEF operon is increased by hydroxyurea and oxidative stress . [More information is available at EcoCyc: EG12381].
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Genomic context

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Sequence:
NC_000913.3 (2803502..2804461)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene glutaredoxin-like protein NrdH Neighboring gene dimanganese-tyrosyl radical cofactor maintenance flavodoxin NrdI Neighboring gene ribonucleoside-diphosphate reductase 2 subunit alpha Neighboring gene glycine betaine ABC transporter ATP binding subunit ProV Neighboring gene glycine betaine ABC transporter membrane subunit ProW Neighboring gene glycine betaine ABC transporter periplasmic binding protein ProX

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. Cloning and sequencing of the genes from Salmonella typhimurium encoding a new bacterial ribonucleotide reductase. Jordan A, et al. J Bacteriol, 1994 Jun. PMID 8195103, Free PMC Article
  2. The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation. Martin JE, et al. Mol Microbiol, 2011 Apr. PMID 21338418, Free PMC Article
  3. A second class I ribonucleotide reductase in Enterobacteriaceae: characterization of the Salmonella typhimurium enzyme. Jordan A, et al. Proc Natl Acad Sci U S A, 1994 Dec 20. PMID 7809142, Free PMC Article
  4. Structural basis for activation of class Ib ribonucleotide reductase. Boal AK, et al. Science, 2010 Sep 17. PMID 20688982, Free PMC Article
  5. An active dimanganese(III)-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase. Cotruvo JA Jr, et al. Biochemistry, 2010 Feb 16. PMID 20070127, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Thus NrdEF supports DNA replication when iron is unavailable to activate the housekeeping NrdAB enzyme.
    Title: The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation.
  2. results strongly suggest that E. coli NrdF is an obligate manganese protein in vivo and that the Mn(III)(2)-Y(*) cofactor assembly pathway
    Title: Escherichia coli class Ib ribonucleotide reductase contains a dimanganese(III)-tyrosyl radical cofactor in vivo.
  3. crystal structure of Mn(II)2-NrdF and Fe(II)2-NrdF reveal different coordination environments; in structures of Mn(II)2-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects NrdI flavin cofactor to the NrdF Mn(II)2 active site
    Title: Structural basis for activation of class Ib ribonucleotide reductase.
  4. Functional long-range proton-coupled electron transfer in ribonucleoside diphosphate reductase occurs via an optimized pathway of amino acids spanning >35 A across the alpha:beta interface.
    Title: Use of 3-aminotyrosine to examine the pathway dependence of radical propagation in Escherichia coli ribonucleotide reductase.
Submit: New GeneRIF Correction

Pathways from PubChem

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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 manganese ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor IEA
Inferred from Electronic Annotation
more info
  
contributes_to ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor IGI
Inferred from Genetic Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in 2'-deoxyribonucleotide biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in deoxyribonucleotide biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within deoxyribonucleotide biosynthetic process IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in ribonucleoside diphosphate metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of ribonucleoside-diphosphate reductase complex IEA
Inferred from Electronic Annotation
more info
  
part_of ribonucleoside-diphosphate reductase complex IGI
Inferred from Genetic Interaction
more info
 PubMed 
part_of ribonucleoside-diphosphate reductase complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
ribonucleoside-diphosphate reductase 2 subunit beta
NP_417162.1

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
    2803502..2804461
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_417162.1 ribonucleoside-diphosphate reductase 2 subunit beta [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_417162.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A8S7TJ10
    Conserved Domains (1) summary
    TIGR04171
    Location:6 → 319
    RNR_1b_NrdF; ribonucleoside-diphosphate reductase, class 1b, beta subunit
Nucleotide Protein
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