clpP
BSGatlas-gene-4038
BSGatlas
Description | Information |
---|---|
Coordinates | 3546234..3546827 |
Genomic Size | 594 bp |
Name | clpP |
Outside Links | SubtiWiki |
BsubCyc | |
Strand | + |
Type | CDS |
SubtiWiki
Description | Information |
---|---|
Alternative Name | clpP |
clpP | |
yvdN | |
Category | SW 3 Information processing |
SW 3.3 Protein synthesis, modification and degradation | |
SW 3.3.7 Proteolysis | |
SW 3.3.7.4 Additional proteins involved in proteolysis | |
SW 4 Lifestyles | |
SW 4.3 Coping with stress | |
SW 4.3.1 General stress proteins (controlled by SigB) | |
SW 4.3.4 Heat shock proteins | |
SW 6 Groups of genes | |
SW 6.4 Phosphoproteins | |
SW 6.4.1 Phosphorylation on an Arg residue | |
Description | ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) |
Enzyme Classifications | EC 3.4.21.92: Endopeptidase Clp |
Function | protein degradation |
Is essential? | no |
Isoelectric point | 5 |
Locus Tag | BSU_34540 |
Molecular weight | 21 |
Name | clpP |
Product | ATP-dependent Clp protease proteolytic subunit |
RefSeq
Description | Information |
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Alternative Locus Tag | BSU34540 |
Description | Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 11722737, 11807061,15317791, 16163393, 21546913, 21969594, 22226636,27749819; Product type e: enzyme |
Enzyme Classifications | EC 3.4.21.92: Endopeptidase Clp |
Functions | 16.11: Scavenge (Catabolism) |
16.3: Control | |
16.6: Maintain | |
16.8: Protect | |
Locus Tag | BSU_34540 |
Name | clpP |
Title | ATP-dependent Clp protease proteolytic subunit;Maxwell's demon |
Type | CDS |
BsubCyc
Description | Information |
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Alternative Name | yvdN |
Citation | Alexopoulos J;Ahsan B;Homchaudhuri L;Husain N;Cheng YQ;Ortega J Structural determinants stabilizing the axial channel of ClpP for substrate translocation. Mol Microbiol 90(1);167-80 (2013) PUBMED: 23927726 |
Brzozowska I;Zielenkiewicz U The ClpXP protease is responsible for the degradation of the Epsilon antidote to the Zeta toxin of the streptococcal pSM19035 plasmid. J Biol Chem 289(11);7514-23 (2014) PUBMED: 24492616 | |
Carney DW;Compton CL;Schmitz KR;Stevens JP;Sauer RT;Sello JK A simple fragment of cyclic acyldepsipeptides is necessary and sufficient for ClpP activation and antibacterial activity. Chembiochem 15(15);2216-20 (2014) PUBMED: 25212124 | |
Chan CM;Hahn E;Zuber P Adaptor bypass mutations of Bacillus subtilis spx suggest a mechanism for YjbH-enhanced proteolysis of the regulator Spx by ClpXP. Mol Microbiol 93(3);426-38 (2014) PUBMED: 24942655 | |
Lee BG;Kim MK;Song HK Structural insights into the conformational diversity of ClpP from Bacillus subtilis. Mol Cells 32(6);589-95 (2011) PUBMED: 22080375 | |
Lee BG;Park EY;Lee KE;Jeon H;Sung KH;Paulsen H;Rubsamen-Schaeff H;Brotz-Oesterhelt H;Song HK Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism. Nat Struct Mol Biol 17(4);471-8 (2010) PUBMED: 20305655 | |
Moliere N;Hossmann J;Schafer H;Turgay K Role of Hsp100/Clp Protease Complexes in Controlling the Regulation of Motility in Bacillus subtilis. Front Microbiol 7;315 (2016) PUBMED: 27014237 | |
Reddy PJ;Sinha S;Ray S;Sathe GJ;Chatterjee A;Prasad TS;Dhali S;Srikanth R;Panda D;Srivastava S Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment. PLoS One 10(4);e0120620 (2015) PUBMED: 25874956 | |
Runde S;Moliere N;Heinz A;Maisonneuve E;Janczikowski A;Elsholz AK;Gerth U;Hecker M;Turgay K The role of thiol oxidative stress response in heat-induced protein aggregate formation during thermotolerance in Bacillus subtilis. Mol Microbiol 91(5);1036-52 (2014) PUBMED: 24417481 | |
Trentini DB;Suskiewicz MJ;Heuck A;Kurzbauer R;Deszcz L;Mechtler K;Clausen T Arginine phosphorylation marks proteins for degradation by a Clp protease. Nature 539(7627);48-53 (2016) PUBMED: 27749819 | |
Comment | 16.3: Control 16.6: Maintain 16.11: Scavenge (Catabolism) 16.8: Protect |
Description | ATP-dependent Clp protease proteolytic subunit |
Enzyme Classifications | EC 3.4.21.92: Endopeptidase Clp |
Gene Ontology | GO:0000166 nucleotide binding |
GO:0004176 ATP-dependent peptidase activity | |
GO:0004252 serine-type endopeptidase activity | |
GO:0005524 ATP binding | |
GO:0005737 cytoplasm | |
GO:0006508 proteolysis | |
GO:0006950 response to stress | |
GO:0008233 peptidase activity | |
GO:0008236 serine-type peptidase activity | |
GO:0016787 hydrolase activity | |
Locus Tag | BSU34540 |
Molecular weight | 21.682 |
Name | clpP |
Nicolas et al. predictions
Description | Information |
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Expression neg. correlated with | new_2212747_2212847, new_2069824_2069977, BSU20929, BSU21340, BSU20928, new_3388289_3388830_c, new_3061289_3061624_c, BSU21700, new_1670054_1671124_c, new_2647355_2647455 |
Expression pos. correlated with | BSU31370, BSU10260, BSU28500, BSU00850, BSU14680, BSU14670, BSU33400, BSU38110, BSU03870, BSU14650 |
Highly expressed condition | (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]. |
(dia5) 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 | |
(Etha) Cells were grown in a synthetic medium (J. Stülke, R. Hanschke, M. Hecker, J Gen Microbiol 139, 2041, Sep, 1993) with 0.2 % glucose as carbon source (Belitsky Minimal Medium/BMM) at 37 °C with vigorous shaking. Stress was applied to exponentially growing cultures at OD500nm of 0.4. Samples were harvested before stress [BMM]; after a rapid temperature up-shift from 37 °C to 48 °C [Heat]; after a temperature down-shift from 37 °C to 18 °C [Cold]. Ethanol stress was imposed by adding ethanol to a final concentration of 4 % (v/v) and cells were harvested 10 minutes after ethanol addition [Etha]. | |
(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 | |
(Heat) Cells were grown in a synthetic medium (J. Stülke, R. Hanschke, M. Hecker, J Gen Microbiol 139, 2041, Sep, 1993) with 0.2 % glucose as carbon source (Belitsky Minimal Medium/BMM) at 37 °C with vigorous shaking. Stress was applied to exponentially growing cultures at OD500nm of 0.4. Samples were harvested before stress [BMM]; after a rapid temperature up-shift from 37 °C to 48 °C [Heat]; after a temperature down-shift from 37 °C to 18 °C [Cold]. Ethanol stress was imposed by adding ethanol to a final concentration of 4 % (v/v) and cells were harvested 10 minutes after ethanol addition [Etha]. | |
(LBtran) Cells were grown in Luria-Bertani medium (Sigma) [LB] at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 2000-fold in fresh pre-warmed medium and samples were collected during the exponential [exp], transition [tran] and stationary [stat] phases of the growth cycle . | |
(LPhT) Cells were harvested (i) during exponential growth in high phosphate defined medium [HPh]; (ii) during exponential growth in low phosphate defined medium [LPh] (J. P. Muller, Z. An, T. Merad, I. C. Hancock, C. R. Harwood, Microbiology 143, 947, Mar, 1997);and (iii) at three hours after the outset of the phosphate-limitation induced stationary phase [LPhT]. | |
(Mt0) 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]. | |
(Salt) Cells were grown in Spizizen’s minimal medium (SMM) at 37 °C with vigorous shaking. Salt was added, to a final concentration of 0.4 M to an exponentially growing culture of cells at OD500 of 0.4. Samples were harvested before [SMM] and 10 minutes after [Salt] NaCl addition. | |
Lowely expressed condition | (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. |
(Cold) Cells were grown in a synthetic medium (J. Stülke, R. Hanschke, M. Hecker, J Gen Microbiol 139, 2041, Sep, 1993) with 0.2 % glucose as carbon source (Belitsky Minimal Medium/BMM) at 37 °C with vigorous shaking. Stress was applied to exponentially growing cultures at OD500nm of 0.4. Samples were harvested before stress [BMM]; after a rapid temperature up-shift from 37 °C to 48 °C [Heat]; after a temperature down-shift from 37 °C to 18 °C [Cold]. Ethanol stress was imposed by adding ethanol to a final concentration of 4 % (v/v) and cells were harvested 10 minutes after ethanol addition [Etha]. | |
(LBGstat) Cells were grown in Luria-Bertani medium (Sigma) supplemented with glucose 0.3 % [LBG] at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 2000-fold in fresh pre-warmed medium and samples were collected during the exponential [exp], transition [tran] and stationary [stat] phases of the growth cycle . | |
(MG+150) A culture of LB medium was inocualted from a frozen glycerol stock of B. subtilis. After few hours at 37oC when the culture was growing exponentially, this culture was used to inoculate M9 minimal medium at several different dilutions usually in the range of 500- to 2000-fold. The dilution range was chosen to ensure that at least one of these M9 precultures had reached an OD600 between 0.5 - 1.0 after overnight incubation. These precultures were then used to inoculate 2.5 L of M9 medium in a 3.1 L KLF bioreactor (Bioengineering AG, Wald, Switzerland) to a starting OD600 of 0.03 – 0.05. Condiions in the bioreactor were rigorously controlled as follows: temperature was controlled at 37 °C; the pH was maintained at exactly 7.2 by automatic titration with 2.0 M KOH and 2.0 M H2SO4, and the dissolved oxygen tension was maintained above 50%. In each nutritional shift experiment cells were grown on the single substrate until the OD600 reached 0.50, at which point the second substrate was added instantaneously (4 g/L L-malate or 3 g/L glucose). The nutrient shifts performed were from glucose to glucose+malate [GM] and from malate to malate+glucose [MG] (Buescher et al., accompanying paper). Cell growth during the course was monitored throughout the experiment by measuring OD600. | |
(T-5.40H) 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]. | |
(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]. | |
(T1.30H) 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]. | |
(T2.0H) 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]. | |
(T2.30H) 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]. | |
Name | clpP |