nrdF
BSGatlas-gene-2038
BSGatlas
Description | Information |
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Coordinates | 1871089..1872078 |
Genomic Size | 990 bp |
Name | nrdF |
Outside Links | SubtiWiki |
BsubCyc | |
Strand | + |
Type | CDS |
SubtiWiki
Description | Information |
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Alternative Name | nrdF |
Category | SW 2 Metabolism |
SW 2.5 Nucleotide metabolism | |
SW 2.5.2 Biosynthesis/ acquisition of nucleotides | |
SW 2.5.2.5 Biosynthesis/ acquisition of nucleotides/ other | |
SW 6 Groups of genes | |
SW 6.1 Essential genes | |
Description | ribonucleoside-diphosphate reductase (beta subunit) |
Enzyme Classifications | EC 1.17.4.1: ribonucleoside-diphosphate reductase |
Function | synthesis of deoxyribonucleoside triphosphates |
Is essential? | yes |
Isoelectric point | 4.66 |
Locus Tag | BSU_17390 |
Molecular weight | 38.2218 |
Name | nrdF |
Product | ribonucleoside-diphosphate reductase (beta subunit) |
RefSeq
Description | Information |
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Alternative Locus Tag | BSU17390 |
Description | Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 12682299, 15937154,16885274, 17395719, 21561096, 22443445, 23402532,24401092, 27920297; Product type e: enzyme |
Enzyme Classifications | EC 1.17.4.1: ribonucleoside-diphosphate reductase |
Functions | 16.2: Construct biomass (Anabolism) |
Locus Tag | BSU_17390 |
Name | nrdF |
Title | ribonucleoside-diphosphate reductase (minorsubunit) |
Type | CDS |
BsubCyc
Description | Information |
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Citation | Boal AK;Cotruvo JA;Stubbe J;Rosenzweig AC The dimanganese(II) site of Bacillus subtilis class Ib ribonucleotide reductase. Biochemistry 51(18);3861-71 (2012) PUBMED: 22443445 |
Castro-Cerritos KV;Yasbin RE;Robleto EA;Pedraza-Reyes M Role of Ribonucleotide Reductase in Bacillus subtilis Stress-Associated Mutagenesis. J Bacteriol 199(4) (2017) PUBMED: 27920297 | |
Cotruvo JA;Stich TA;Britt RD;Stubbe J Mechanism of assembly of the dimanganese-tyrosyl radical cofactor of class Ib ribonucleotide reductase: enzymatic generation of superoxide is required for tyrosine oxidation via a Mn(III)Mn(IV) intermediate. J Am Chem Soc 135(10);4027-39 (2013) PUBMED: 23402532 | |
Parker MJ;Zhu X;Stubbe J Bacillus subtilis class Ib ribonucleotide reductase: high activity and dynamic subunit interactions. Biochemistry 53(4);766-76 (2014) PUBMED: 24401092 | |
Zhang Y;Stubbe J Bacillus subtilis class Ib ribonucleotide reductase is a dimanganese(III)-tyrosyl radical enzyme. Biochemistry 50(25);5615-23 (2011) PUBMED: 21561096 | |
Comment | 16.2: Construct biomass (Anabolism) 10/23/2009 (keseler) Information from the deleted enzymatic-reaction frame, upon complex formation: Basis for assignment: EC-NUMBER . |
Description | ribonucleoside-diphosphate reductase (minor subunit) |
Gene Ontology | GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
GO:0005971 ribonucleoside-diphosphate reductase complex | |
GO:0006260 DNA replication | |
GO:0009186 deoxyribonucleoside diphosphate metabolic process | |
GO:0009263 deoxyribonucleotide biosynthetic process | |
GO:0016491 oxidoreductase activity | |
GO:0046872 metal ion binding | |
GO:0055114 oxidation-reduction process | |
Locus Tag | BSU17390 |
Molecular weight | 38.379 |
Name | nrdF |
Nicolas et al. predictions
Description | Information |
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Expression neg. correlated with | BSU24590, BSU27450, BSU18240, BSU27460, BSU18250, new_1211286_1211370, BSU18239, new_3316213_3316329_c, BSU27440, BSU18230 |
Expression pos. correlated with | BSU17380, BSU17400, BSU17370, BSU22770, BSU16570, BSU25510, BSU06690, new_88636_88726, BSU22780, BSU41040 |
Highly expressed condition | (BC) Cultures were inoculated from frozen glycerol stocks and grown overnight in LB at 37°C. These cultures were thendiluted, plated onto LB plates, and incubated for 16 h at 37°C. Cells were harvested from plates containing individual colonies [BI] andfrom plates with confluen growth [BC]. |
(BI) Cultures were inoculated from frozen glycerol stocks and grown overnight in LB at 37°C. These cultures were thendiluted, plated onto LB plates, and incubated for 16 h at 37°C. Cells were harvested from plates containing individual colonies [BI] andfrom plates with confluen growth [BC]. | |
(C30) Cellsgrown overnight on LB agar plates at 30°Cwere harvested and used to inoculate pre-warmed minimal medium at OD600 of 0.5 (D. Dubnau, R. Davidoff-Abelson, J Mol Biol 56, 209, Mar 14, 1971). After growth at 37°C with vigorous shaking, cells were diluted ten times in fresh pre-warmed minimal medium and samples were harvested after a period of 30 minutes [C30] , i.e. before maximal induction of competence, and after a period of 90 minutes [C90], i.e. when competence induction was maximal. | |
(dia15) Diamide was added to an exponentially growing culture (OD600 approx. 0.6) at a sub-lethal concentration(0.5 mM) and growth continued at 37°C with vigorous shaking. Samples were collected 0, 5 and 15 minutes after diamide addition [dia0, dia5 and dia15]. | |
(Diami) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition | |
(G135) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180]. | |
(G180) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180]. | |
(H2O2) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition | |
(Paraq) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition | |
(Sw) Exponentially growing cells were spotted on 1 % agar LB plates and incubated at 37°C. Swarming cells were collected after 16 hours. | |
Lowely expressed condition | (M0t90) Cells were grown in LB medium at 37°C with vigorous shaking. An exponentially growing culture (O.D.600 approx. 0.25) was divided: one culture acted as the control [no mitomycin C , M0] while mitomycin was added to the second culture to a final concentration of 40 ng/ml [mitomycin, M40]. Samples were harvested at 0, 45 and 90 minutes after mitomycin addition [t0, t45 and t90]. |
(M40t90) Cells were grown in LB medium at 37°C with vigorous shaking. An exponentially growing culture (O.D.600 approx. 0.25) was divided: one culture acted as the control [no mitomycin C , M0] while mitomycin was added to the second culture to a final concentration of 40 ng/ml [mitomycin, M40]. Samples were harvested at 0, 45 and 90 minutes after mitomycin addition [t0, t45 and t90]. | |
(M9stat) Cells were grown in M9 supplemented with glucose (0.3 %) at 37°C with vigorous shaking. The composition of the M9 minimal medium is (per liter): 8.5 g Na2HPO4.2H20, 3 g KH2PO4, 1 g NH4Cl and 0.5 g NaCl. The following solutions were individually sterilized and added (volumes per liter of medium): 1 ml 0.1 M CaCl2.2H2O, 1 ml 1 M MgSO4.7H2O, 1 ml 50 mM Fe-Citrate. Also added was 10 ml of a trace salts solution containing (per liter): 170 mg ZnCl2, 100 mg MnCl2.4H2O, 60 mg CoCl2.6H2O, 60 mg Na2MoO4.2H2O and 43 mg CuCl2.2H2O. Overnight cultures were diluted 2000-fold in pre-warmed M9 medium and samples were harvested during exponential growth [M9exp], at the transition phase [M9tran] and during stationary phase [M9stat]. | |
(S4) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments. | |
(S5) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments. | |
(S6) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments. | |
(S7) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments. | |
(S8) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments. | |
(T0.30H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H]. | |
(T1.0H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H]. | |
Name | nrdF |
KEGG Pathways
Description | Information |
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Pathway | Purine metabolism (ko00230) |
Pyrimidine metabolism (ko00240) | |
Metabolic pathways (ko01100) |