SubtiBank SubtiBank
nrdE
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nrdE

ribonucleoside-diphosphate reductase (alpha subunit), control of DNA/cell mass ratio
locus
BSU_17380
pI
5.93
mw
80.50 kDa
protein length
700 aa Sequence Blast
gene length
2103 bp Sequence Blast
function
synthesis of deoxyribonucleoside triphosphates
product
ribonucleoside-diphosphate reductase (alpha subunit)
essential
yes
ec
1.17.4.1
synonyms

Genomic Context

      

categories

  • [category|SW 2|Metabolism] → [category|SW 2.5|Nucleotide metabolism] → [category|SW 2.5.2|Biosynthesis/ acquisition of nucleotides] → [category|SW 2.5.2.5|Biosynthesis/ acquisition of nucleotides/ other]
  • [category|SW 6|Groups of genes] → [category|SW 6.1|Essential genes]
  • Gene

    Coordinates
    1,868,969 1,871,071

    Phenotypes of a mutant

  • essential [Pubmed|12682299]
  • The protein

    Catalyzed reaction/ biological activity

  • [thioredoxin]-disulfide + 2'-deoxyribonucleoside 5'-diphosphate + H2O --> [thioredoxin]-dithiol + ribonucleoside 5'-diphosphate (according to UniProt)
  • required for stationary-phase mutagenesis [Pubmed|27920297]
  • Protein family

  • ribonucleoside diphosphate reductase large chain family (with [protein|FD4CD7DB35AA20DBBEC0A4DA5D88282D89CCDA6D|NrdEB], according to UniProt)
  • Paralogous protein(s)

  • [protein|FD4CD7DB35AA20DBBEC0A4DA5D88282D89CCDA6D|NrdEB]
  • Kinetic information

  • Steady-state kinetics [Pubmed|29712847]
  • Effectors of protein activity

  • ATP stimulates CDP and UDP reduction [Pubmed|29712847,24401092]
  • dATP at concentrations up to ~10 M stimulate CDP and UDP reduction, while higher concentrations inhibit this activity, inhibition by dATP is enhanced by binding of dAMP to the N-terminal domain of [protein|3B68CE8E9A35997B45E437A316996D585E43B76B|NrdE] [Pubmed|31201319,29712847,24401092]
  • TTP stimulates GDP reduction [Pubmed|29712847]
  • dGTP stimulates ADP reduction [Pubmed|29712847]
  • Structure

  • [PDB|6CGL] (pH 4, dAMP bound) [Pubmed|29712847]
  • [PDB|6CGM] (pH 7, apo-protein) [Pubmed|29712847]
  • [PDB|6CGN] (pH 7, dAMP bound) [Pubmed|29712847]
  • [PDB|6MT9] (TTP in substrate specificity site, ADP in inhibitory site (M-site), and ATP in activity site (I-site)) [Pubmed|31201319]
  • [PDB|6MV9] (TTP in substrate specificity site, ADP in inhibitory site (M-site)) [Pubmed|31201319]
  • [PDB|6MVE] (TTP in S-site, ADP in M-site, ATP in I-site, and C-terminal cysteine residues captured in active site) [Pubmed|31201319]
  • [PDB|6MW3] (cyro-EM structure of inhibitory filament formed with [protein|CD2D14FE9C10544E7C350167EBDBD941B898051D|NrdF] [Pubmed|31201319]
  • [PDB|6MYX] (cryo-EM structure of inhibitory filament) [Pubmed|31201319]
  • Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation [PubMed|17981983]
  • Expression and Regulation

    Operons

    genes
    [gene|1EA0595C74359A36B9161CFD531CA894C5E66E25|nrdI]-[gene|3B68CE8E9A35997B45E437A316996D585E43B76B|nrdE]-[gene|CD2D14FE9C10544E7C350167EBDBD941B898051D|nrdF]-[gene|8C2A08A8395B72CCC9D03A8154602B8F3B77A1AA|ymaB]
    description
    [Pubmed|16885274]

    sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|16885274], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]
  • regulatory mechanism

  • [protein|1E829D639BADDC6BDC9B5FB4C97A632A53FDDB24|ResD]: activation, [Pubmed|16885274], in [regulon|1E829D639BADDC6BDC9B5FB4C97A632A53FDDB24|ResD regulon]
  • [protein|FD4E988BB73F6476CCEA4C521F343D6F8CBA457F|NrdR]: repression, (predicted) [Pubmed|15949864], in [regulon|FD4E988BB73F6476CCEA4C521F343D6F8CBA457F|NrdR regulon]
  • [protein|00BCAAE16576DC5426A652580C69A570FC7A1C2C|PerR]: transcription repression, [Pubmed|27920297], in [regulon|00BCAAE16576DC5426A652580C69A570FC7A1C2C|PerR regulon]
  • regulation

  • expressed under anaerobic conditions ([protein|search|ResD]) [Pubmed|16885274]
  • additional information

  • A [protein|search|ncRNA] is predicted between '[protein|search|ymzA]' and '[protein|search|nrdI]' [PubMed|20525796]
  • view in new tab

    genes
    [gene|93FA602438546FD6201FAB5BD19DB5DEB5965E48|ymzA]-[gene|1EA0595C74359A36B9161CFD531CA894C5E66E25|nrdI]-[gene|3B68CE8E9A35997B45E437A316996D585E43B76B|nrdE]-[gene|CD2D14FE9C10544E7C350167EBDBD941B898051D|nrdF]-[gene|8C2A08A8395B72CCC9D03A8154602B8F3B77A1AA|ymaB]
    description
    [Pubmed|22383849]
    view in new tab

    labs

  • [SW|Elisabeth Härtig], Braunschweig, Germany [http://www.tu-braunschweig.de/ifm/abt/jahn/groups/bs Homepage]
  • References

    Reviews

  • 17229208
  • Original Publications

  • 16885274,8969495,24401092,21561096,12818204,15949864,27920297,28624879,29712847,31201319