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Information on EC 2.7.6.5 - GTP diphosphokinase
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2.7.6.5 GTP diphosphokinaseIUBMB Comments
GDP can also act as acceptor.
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Word Map
- 2.7.6.5
- rela
- rsh
-
ribosome-dependent
-
pppgpp0
-
a-site
- 3'-diphosphate
- tetraphosphate
-
actinorhodine
-
rela-spot
- mupirocin
-
rela-dependent
- thiostrepton
- drug development
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
(p)ppGpp synthase, (p)ppGpp synthetase, (p)ppGpp synthetase I, (p)ppGpp synthetase II, (p)ppGpp synthetase/hydrolase, alarmone synthetase, ATP-GTP 3'-diphosphotransferase, ATP:GTP 3'-pyrophosphotransferase, ATP:GTP pyrophosphoryl transferase, GPSI, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
(p)ppGpp synthase
(p)ppGpp synthetase
(p)ppGpp synthetase I
-
-
-
-
(p)ppGpp synthetase II
-
-
-
-
alarmone synthetase
ATP-GTP 3'-diphosphotransferase
-
-
-
-
ATP:GTP 3'-pyrophosphotransferase
ATP:GTP pyrophosphoryl transferase
GPSI
-
-
-
-
GPSII
-
-
-
-
GTP pyrophosphokinase
guanosine 3',5'-polyphosphate synthase
-
-
-
-
guanosine 3',5'-polyphosphate synthetase
-
-
-
-
guanosine 5',3'-polyphosphate synthetase
-
-
-
-
guanosine pentaphosphate synthetase
-
-
-
-
ppGpp synthase I
Rel
RelA
RelMtb
SAS 1
SAS 2
SAS1
SF
small alarmone synthase 1
small alarmone synthase 2
small alarmone synthetase 1
stringent factor
YjbM
YwaC
(p)ppGpp synthetase
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
-
-
GTP pyrophosphokinase
-
-
-
-
Rel
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
-
-
stringent factor
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
GDP can also act as acceptor
-
-
-
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
bifunctional enzyme, additionally has polynucleotide phosphorylase activities
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
the catalytic pathway of (p)ppGpp synthesis involves a sequentially ordered substrate binding, activation of ATP in a strained conformation, and transfer of diphosphate through a nucleophilic substitution (SN2) reaction. pppGpp, but not ppGpp, positively regulates the enzyme at an allosteric site
-
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
the catalytic pathway of (p)ppGpp synthesis involves a sequentially ordered substrate binding, activation of ATP in a strained conformation, and transfer of diphosphate through a nucleophilic substitution (SN2) reaction. pppGpp, but not ppGpp, positively regulates the enzyme at an allosteric site
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
diphosphate transfer
diphosphate transfer
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
ATP:GTP 3'-diphosphotransferase
GDP can also act as acceptor.
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CAS REGISTRY NUMBER
COMMENTARY
63690-89-1
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2'-methyl-ATP + GTP
2'-methyl-AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
-
?
8-bromo-ATP + GTP
8-bromo-AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
-
?
ATP + guanosine 5'-tetraphosphate
AMP + guanosine 3'-diphosphate 5'-tetraphosphate
-
-
-
-
?
ATP + GDP
AMP + guanosine 3',5'-bis-diphosphate
-
the enzyme utilizes GDP less efficiently than GTP
-
-
?
ATP + GDP
AMP + guanosine 3',5'-bis-diphosphate
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
the enzyme utilizes GDP less efficiently than GTP
-
-
?
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
-
preferred substrate
i.e ppGpp
?
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
-
preferred substrate
-
-
?
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
-
-
-
?
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
i.e. pppGpp
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
RelA-mediated guanosine 3'-diphosphate 5'-triphosphate synthesis requires the presence of an uncharged tRNAVal in the A-Site of a mRNA programmed ribosome
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
high degree of specificity for GTP as a pyrophosphate acceptor, with no measurable turnover for GDP
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
the enzyme uses GTP approximately twice as well as GDP
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
the enzyme uses GTP approximately twice as well as GDP
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
?
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
-
-
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
-
bifunctional enzyme with synthetase and hydrolase activities
-
-
r
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
-
-
-
-
?
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
-
-
-
?
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
-
-
-
?
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
-
-
-
-
?
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
-
-
-
?
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
-
-
-
?
additional information
?
-
-
the enzyme is bifunctional showing synthase activity forming ppGpp and pppGpp, and hydrolase activity with the two compounds resulting in formation of GTP or GDP and diphosphate
-
-
-
additional information
?
-
-
the enzyme is bifunctional showing synthase activity forming ppGpp and pppGpp, and hydrolase activity with the two compounds resulting in formation of GTP or GDP and diphosphate
-
-
-
additional information
?
-
-
no substrate: 5'(beta,gamma-imino)triphosphate, 1,N6-ethyladenosine triphosphate, no diphosphate acceptors: ATP, UTP, CTP, dGTP, dGDP, 2'-O-methyl-GDP, 7-methyl-GDP
-
-
-
additional information
?
-
-
responsible for the synthesis of guanosine 3',5'-bisdiphosphate during stringent response to amino acid starvation
-
-
-
additional information
?
-
-
(p)ppGpp synthetase II is responsible for (p)ppGpp accumulation during carbon source downshift
-
-
-
additional information
?
-
the enzyme transfers a diphosphate from ATP to GDP or GTP to synthesize guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate (pppGpp), respectively. Enzyme RelMtb also encodes a second, distinct catalytic domain that hydrolyzes (p)ppGpp into diphosphate and GDP or GTP
-
-
-
additional information
?
-
the enzyme transfers a diphosphate from ATP to GDP or GTP to synthesize guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate (pppGpp), respectively. Enzyme RelMtb also encodes a second, distinct catalytic domain that hydrolyzes (p)ppGpp into diphosphate and GDP or GTP
-
-
-
additional information
?
-
-
the enzyme also possesses a potent Mn2+-dependent guanosine tetraphosphate hydrolysis activity, with complete hydrolysis to GDP and diphosphate
-
-
-
additional information
?
-
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
the enzyme also possesses a potent Mn2+-dependent guanosine tetraphosphate hydrolysis activity, with complete hydrolysis to GDP and diphosphate
-
-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
P9WHG9
-
-
-
?
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
P9WHG9
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
O31611, O54408, P39583
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
O31611, O54408, P39583
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
Q5NEV0
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
-
-
-
-
-
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
P9WHG9
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
P9WHG9
-
-
-
?
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
-
-
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
-
bifunctional enzyme with synthetase and hydrolase activities
-
-
r
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
-
-
-
-
?
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
P9WHG9
-
-
-
?
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
P9WHG9
-
-
-
?
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
-
-
-
-
?
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
P9WHG9
-
-
-
?
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
P9WHG9
-
-
-
?
additional information
?
-
-
responsible for the synthesis of guanosine 3',5'-bisdiphosphate during stringent response to amino acid starvation
-
-
-
additional information
?
-
-
(p)ppGpp synthetase II is responsible for (p)ppGpp accumulation during carbon source downshift
-
-
-
additional information
?
-
P9WHG9
the enzyme transfers a diphosphate from ATP to GDP or GTP to synthesize guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate (pppGpp), respectively. Enzyme RelMtb also encodes a second, distinct catalytic domain that hydrolyzes (p)ppGpp into diphosphate and GDP or GTP
-
-
-
additional information
?
-
P9WHG9
the enzyme transfers a diphosphate from ATP to GDP or GTP to synthesize guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate (pppGpp), respectively. Enzyme RelMtb also encodes a second, distinct catalytic domain that hydrolyzes (p)ppGpp into diphosphate and GDP or GTP
-
-
-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
Mg2+
-
required as a counter-ion for the nucleoside substrate, excess of Mg2+ is inhibitory
Mg2+
-
the magnesium concentration also affects the binding states of the tRNAs on the ribosome
Mg2+
-
the optimal concentration for pppGpp synthesis is approximately equal to the total concentration of nucleotide substrates([ATP] + [GTP])
Mg2+
-
the enzyme exploits a single Mg2+ ion to catalyze guanosine 3'-diphosphate 5'-triphosphate synthesis
Mg2+
-
essential for activation, the enzyme has a single Mg2+ binding site
Mn2+
-
the optimal concentration for pppGpp synthesis is approximately one-half of the total concentration of nucleotide substrates([ATP] + [GTP])
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Mg2+
-
required as a counter ion for the nucleoside substrate, excess of Mg2+ is inhibitory
Mg2+
-
the enzyme shows a marked decrease in guanosine tetraphosphate synthesis activity with increasing Mg2+ ion concentration
tetracycline
-
endogenous diphoyphoryl transferase activity; ribosome-dependent activity
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dCDP
slightly stimulates synthesis of guanosine 3'-diphosphate 5'-triphosphate, inhibits polynucleotide phosphorylase activities of enzyme
ethanol
-
little activity unless activated either by a complex of 70S ribosomes, mRNA and uncharged tRNA or by a solvent like ethanol at approximately 20%
guanosine-5',3'-dibisphosphate
ppGpp, potential allosteric regulator, activates the enzyme with an EC50 of 0.060 mM
tRNA
-
uncharged or charged, stimulation, level of stimulation is greater in presence of RNA and poly(U) together than with either RNA alone
mRNA
-
little activity unless activated either by a complex of 70S ribosomes, mRNA and uncharged tRNA or by a solvent like ethanol at approximately 20%
mRNA
-
synthetic, e.g. poly(U), stimulates, level of stimulation is greater in presence of RNA and poly(U) together than with either RNA alone, no activation by ribosomes
additional information
-
little activity unless activated either by a complex of 70S ribosomes, mRNA and uncharged tRNA or by a solvent like ethanol at approximately 20%
-
additional information
-
addition of template, unacylated tRNA and ribosomes to the activity assay stimulates SF 30fold when using optimal conditions, activity of SF increases threefold in the presence of twice salt-washed tight-couple ribosomes and twofold in the presence of reassociated ribosomes compared to the endogenous activity of the enzyme
-
additional information
-
ribosome complexes formed with tight binding tRNAVal stimulate enzyme activity at lower concentrations than that required for ribosome complexes formed with the weaker binding tRNAPhe
-
additional information
activation of Francisella tularensis RelA by stalled ribosomal complexes formed with ribosomes purified from Escherichia coli MRE600, and significantly weaker activation with ribosomes isolated from Francisella philomiragia
-
additional information
-
GPS I can be activated by incubation with crude mycelial extract, activation is partially inhibited by the inclusion of trypsin inhibitor in reaction mixture; no activation by ribosomes
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3
guanosine 3'-diphosphate 5'-diphosphate
-
pH 7.5, 37°C, recombinant enzyme
2
guanosine 3'-diphosphate 5'-triphosphate
-
pH 7.5, 37°C, recombinant enzyme
0.259 - 0.344
ATP
pH 8.0, 30°C, recombinant enzyme
0.67
GTP
-
fragment 1-394 monomer; fragment 1-394 + tRNA; fragment 1-394 + tRNA + ribosomes + poly(U)
0.78
GTP
-
fragment 87-394; fragment 87-394 + tRNA; fragment 87-394 + tRNA + ribosomes + poly(U)
0.801 - 1.024
GTP
pH 8.0, 30°C, recombinant enzyme
additional information
additional information
steady-state kinetic analysis, saturation activity curves best fit a sigmoidal function, the kinetic profile can result from allosteric regulation, overview
-
additional information
additional information
-
alarmone synthesis in SAS1 proceeds in a highly cooperative manner
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.47
GTP
-
fragment 87-394; fragment 87-394 + tRNA; fragment 87-394 + tRNA + ribosomes + poly(U)
0.66
GTP
-
fragment 1-394 monomer; fragment 1-394 + tRNA; fragment 1-394 + tRNA + ribosomes + poly(U)
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
2 different enzymes: (p)ppGpp synthetase I, (p)ppGpp synthetase II
-
-
brenda
bifunctional (p)ppGpp synthase/hydrolase SpoT, catalyzes reactions of EC 2.7.6.5 and EC 3.1.7.2
UniProt
brenda
bifunctional (p)ppGpp synthase/hydrolase SpoT, catalyzes reactions of EC 2.7.6.5 and EC 3.1.7.2
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
the C-terminal domain interacts with the ribosome, which is largely dependent on the TGS motif
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
the enzyme RelA belongs to the RSH superfamily, also comprising members such as RelA/SpoT homologue, (p)ppGpp synthetase I, SpoT, and (p)ppGpp synthetase II. The RSH enzyme family controls concentrations of the alarmones (p)ppGpp (guanosine penta- or tetra-phosphate)
evolution
-
the enzyme belongs to the RSH superfamily, which controls concentrations of the alarmones (p)ppGpp (guanosine penta- or tetra-phosphate)
evolution
-
the enzyme belongs to the RSH superfamily, which controls concentrations of the alarmones (p)ppGpp (guanosine penta- or tetra-phosphate)
-
malfunction
Mycobacterium tuberculosis strains expressing the synthetase-dead RelMtb H344Y mutant do not persist in mice. Deletion of a second predicted (p)ppGpp synthetase has no effect on pathogenesis, demonstrating. Expression of an allele encoding the hydrolase-dead RelMtb mutant, RelMtb H80A, decreases the growth rate of Mycobacterium tuberculosis and changes the colony morphology of the bacteria. RelMtb H80A expression during acute or chronic Mycobacterium tuberculosis infection in mice is lethal to the infecting bacteria. Phenotypes, overview
malfunction
GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes. Loss of the (p)ppGpp synthetase activity results in a failure of Bacillus subtilis to grow on minimal medium and causes the requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition; GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes. Loss of the (p)ppGpp synthetase activity results in a failure of Bacillus subtilis to grow on minimal medium and causes the requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition; GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes. Loss of the (p)ppGpp synthetase activity results in a failure of Bacillus subtilis to grow on minimal medium and causes the requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
malfunction
-
GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes. Loss of the (p)ppGpp synthetase activity results in a failure of Bacillus subtilis to grow on minimal medium and causes the requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition; GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes. Loss of the (p)ppGpp synthetase activity results in a failure of Bacillus subtilis to grow on minimal medium and causes the requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition; GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes. Loss of the (p)ppGpp synthetase activity results in a failure of Bacillus subtilis to grow on minimal medium and causes the requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
-
malfunction
-
Mycobacterium tuberculosis strains expressing the synthetase-dead RelMtb H344Y mutant do not persist in mice. Deletion of a second predicted (p)ppGpp synthetase has no effect on pathogenesis, demonstrating. Expression of an allele encoding the hydrolase-dead RelMtb mutant, RelMtb H80A, decreases the growth rate of Mycobacterium tuberculosis and changes the colony morphology of the bacteria. RelMtb H80A expression during acute or chronic Mycobacterium tuberculosis infection in mice is lethal to the infecting bacteria. Phenotypes, overview
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physiological function
in Mycobacterium tuberculosis, the stringent response to amino acid starvation is mediated by the enzyme Rel (RelMtb), which transfers a diphosphate from ATP to GDP or GTP to synthesize guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate (pppGpp), respectively. (p)ppGpp then influences numerous metabolic processes. RelMtb also encodes a second, distinct catalytic domain that hydrolyzes (p)ppGpp into diphosphate and GDP or GTP. RelMtb is required for chronic Mycobacterium tuberculosis infection in C57BL/6 mice. The RelMtb (p)ppGpp synthetase activity is required for maintaining bacterial titers during chronic infection, RelMtb is the major contributor to (p)ppGpp production during infection, RelMtb (p)ppGpp hydrolase activity is essential for acute and chronic infection of mice
physiological function
guanosine 3'-diphosphate 5'-triphosphate, (p)ppGpp, synthesis is required for amino acid prototrophy; guanosine 3'-diphosphate 5'-triphosphate, (p)ppGpp, synthesis is required for amino acid prototrophy; guanosine 3'-diphosphate 5'-triphosphate, (p)ppGpp, synthesis is required for amino acid prototrophy
physiological function
-
guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively termed (p)ppGpp, act as alarmones that globally reprogram cellular physiology during various stress conditions. Enzymes of the RelA/SpoT homology (RSH) family synthesize (p)ppGpp by transferring diphosphate from ATP to GDP or GTP. ppGpp and pppGpp execute different functional roles
physiological function
the level of ppGpp controls the length of diauxic lag via control of the level of acetyl phosphate
physiological function
overexpression of isoform RSH3 cDNA in the rsh2rsh3 mutant background leads to approximately threefold higher ppGpp levels than in wild-type. Upon transition to nitrogen-deficient conditions, the mutant shows reduction of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) contents, and effective and maximum quantum yield of photosystem II compared with wild-type. The mutant also shows obvious changes in key metabolite levels including some amino acid contents
physiological function
in vivo, under relaxed conditions, as well as in vitro, the C-terminal regulatory domain CTD inhibits synthetase activity but is not required for hydrolase activity. Under stringent conditions, the CTD is essential for (p)ppGpp synthesis. A mutant lacking the CTD exhibits net hydrolase activity when expressed in Staphylococcus aureus but net (p)ppGpp synthetase activity when expressed in Escherichia coli. The conserved TGS and DC motifs within the CTD are required for correct stringent response, whereas the conserved ACT motif is dispensable. The enzyme primarily exists in a synthetase-off/hydrolase-on state
physiological function
-
guanosine 3'-diphosphate 5'-triphosphate, (p)ppGpp, synthesis is required for amino acid prototrophy; guanosine 3'-diphosphate 5'-triphosphate, (p)ppGpp, synthesis is required for amino acid prototrophy; guanosine 3'-diphosphate 5'-triphosphate, (p)ppGpp, synthesis is required for amino acid prototrophy; guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively termed (p)ppGpp, act as alarmones that globally reprogram cellular physiology during various stress conditions. Enzymes of the RelA/SpoT homology (RSH) family synthesize (p)ppGpp by transferring diphosphate from ATP to GDP or GTP. ppGpp and pppGpp execute different functional roles
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physiological function
-
in Mycobacterium tuberculosis, the stringent response to amino acid starvation is mediated by the enzyme Rel (RelMtb), which transfers a diphosphate from ATP to GDP or GTP to synthesize guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate (pppGpp), respectively. (p)ppGpp then influences numerous metabolic processes. RelMtb also encodes a second, distinct catalytic domain that hydrolyzes (p)ppGpp into diphosphate and GDP or GTP. RelMtb is required for chronic Mycobacterium tuberculosis infection in C57BL/6 mice. The RelMtb (p)ppGpp synthetase activity is required for maintaining bacterial titers during chronic infection, RelMtb is the major contributor to (p)ppGpp production during infection, RelMtb (p)ppGpp hydrolase activity is essential for acute and chronic infection of mice
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additional information
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mechanism and allosteric regulation of the highly cooperative enzyme from Bacillus subtilis, overview. Analysis of the catalytic mechanism of (p)ppGpp synthesis by oligomeric and highly cooperative small alarmone synthetase 1 (SAS1) at atomic resolution, structural and biochemical analysis reveals that only pppGpp, but not ppGpp, positively affects the activity of the enzyme
additional information
-
mechanism and allosteric regulation of the highly cooperative enzyme from Bacillus subtilis, overview. Analysis of the catalytic mechanism of (p)ppGpp synthesis by oligomeric and highly cooperative small alarmone synthetase 1 (SAS1) at atomic resolution, structural and biochemical analysis reveals that only pppGpp, but not ppGpp, positively affects the activity of the enzyme
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Show AA Sequence and Transmembrane Helices (7313 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Bacillus subtilis (strain 168)
Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
Escherichia coli (strain K12)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
47000
-
1 * 47000, GPS II, produced by proteolysis of the larger 88000 MW form, denaturing PAGE, 1 * 88000, GPS I, denaturing PAGE
74000
88000
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1 * 47000, GPS II, produced by proteolysis of the larger 88000 MW form, denaturing PAGE, 1 * 88000, GPS I, denaturing PAGE
128000
recombinant His-tagged enzyme, gel filtration
74000
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synthetase II, sucrose density gradient centrifugation
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
2 * 74000, recombinant His-tagged enzyme, SDS-PAGE
homotetramer
monomer
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1 * 47000, GPS II, produced by proteolysis of the larger 88000 MW form, denaturing PAGE, 1 * 88000, GPS I, denaturing PAGE
homotetramer
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domain structure and three-dimensional homology modelling, sequence comparisons, crystal structure analysis, overview
homotetramer
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domain structure and three-dimensional homology modelling, sequence comparisons, crystal structure analysis, overview
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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
purified enzyme in presence of ATP and GTP, 1 week, X-ray diffraction structure determination and analysis at 2.94 A resolution
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the crystallographic asymmetric unit contains two copies of RelSeq 1-385, two catalytic domains are clearly evident within each monomer, with the hydrolase (residues 5-159) and the synthetase (residues 176-371) domains joined by an overlapping central 3-helix bundle (residues 135-195)
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D264G
site-directed mutagenesis, the mutation specifically abolishes (p)ppGpp synthetase activity without affecting other potential functions of the protein. Loss of the (p)ppGpp synthetase activity results in failure to grow on minimal medium and requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
D72G
site-directed mutagenesis, the mutation specifically abolishes (p)ppGpp synthetase activity without affecting other potential functions of the protein. Loss of the (p)ppGpp synthetase activity results in failure to grow on minimal medium and requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
D87G
site-directed mutagenesis, the mutation specifically abolishes (p)ppGpp synthetase activity without affecting other potential functions of the protein. Loss of the (p)ppGpp synthetase activity results in failure to grow on minimal medium and requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
D264G
-
site-directed mutagenesis, the mutation specifically abolishes (p)ppGpp synthetase activity without affecting other potential functions of the protein. Loss of the (p)ppGpp synthetase activity results in failure to grow on minimal medium and requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
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D72G
-
site-directed mutagenesis, the mutation specifically abolishes (p)ppGpp synthetase activity without affecting other potential functions of the protein. Loss of the (p)ppGpp synthetase activity results in failure to grow on minimal medium and requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
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D87G
-
site-directed mutagenesis, the mutation specifically abolishes (p)ppGpp synthetase activity without affecting other potential functions of the protein. Loss of the (p)ppGpp synthetase activity results in failure to grow on minimal medium and requirement for valine, leucine, isoleucine, threonine, and methionine, and a weaker requirement for arginine, histidine, and tryptophan addition
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E319Q
mutant lacks (p)ppGpp synthase activity but retains hydrolase activity
H344Y
H80A
H344Y
-
site-directed mutagenesis, the mutant enzyme shows no synthase activity
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H80A
-
site-directed mutagenesis, the mutant enzyme shows no hydrolase activity
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D264G
-
eliminates detectable synthetase activity without appreciably altering the hydrolase activity
E323Q
-
eliminates detectable synthetase activity without appreciably altering the hydrolase activity
additional information
H344Y
site-directed mutagenesis, the mutant enzyme shows no synthase activity
H80A
site-directed mutagenesis, the mutant enzyme shows no hydrolase activity
additional information
generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine; generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine; generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine
additional information
generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine; generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine; generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine
additional information
-
generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine; generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine; generation of strain JDW1464 (relAD264G ywaCD87GyjbMD72G) by substituting a conserved aspartic acid residue in each of the three (p)ppGpp synthetases, corresponding to D264 in RelA, D87 in YwaC, and D72 in YjbM, with glycine
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additional information
-
fragments 1-203 (22.7 kDa) and 1-181 (20.1 kDa) possess hydrolytic activity but are incapable of synthesis activity, fragment 1-156 (17.3 kDa) is not capable of either synthesis or hydolytic activity, relative acticity of fragment 1-181 decreases approximately 130fold compared to that of the wild type, fragment 87-394 (35.1 kDa) has only synthesis activity, fragment 1-394 (44.6 kDa) and 1-450 are capable of synthesis and hydrolysis, the trimer state of fragment 1-394 appears to be a catalytically less efficient state than the monomer state, fragment 395-738 is devoid of any activity
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the purified SF is stored in the freezer, at a concentration of 1.0 mg/ml in 20% (v/v) glycerol, without forming a precipitate or loss of activity
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21 (DE3) pLysS by nickel affinity chromatography and gel filtration
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
expression of the N-terminal catalytic fragment (residues 1-385) in Escherichia coli BL21
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gene relA, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21 (DE3) pLysS
gene relA, recombinant expression of wild-type and mutant enzymes in Escherichia coli; gene yjbM, recombinant expression of wild-type and mutant enzymes in Escherichia coli; gene ywaC, recombinant expression of wild-type and mutant enzymes in Escherichia coli
gene yjbM, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
CodY-independent activation of transcription of the ywaA operon, overview
the transcription factor CodY represses the ywaA operon, overview
CodY-independent activation of transcription of the ywaA operon, overview
the transcription factor CodY represses the ywaA operon, overview
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
the purified enzyme is renatured by stepwise dialysis in buffers containing sequentially decreasing concentrations of urea (50mM Tris-HCl, pH 7.9 at 4°C, 150 mM NaCl, 100 mM imidazole, and 4 M, 2 M, and 0 M urea, in that order)
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
-
the structural knowledge of the self-regulatory mechanisms for controlling the opposing catalytic activities of RelSeq can be used to design specific inhibitors that interfere with either of the active sites and may have the potential of being developped into powerful antibacterial drugs
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sy, J.; Akers, H.
Purification and properties of guanosine 5,3-polyphosphate synthetase from Bacillus brevis
Biochemistry
15
4399-4403
1976
Brevibacillus brevis
brenda
Fehr, S.; Richter, D.
Stringent response of Bacillus stearothermophilus: evidence for the existence of two distinct guanosine 3,5-polyphosphate synthetases
J. Bacteriol.
145
68-73
1981
Geobacillus stearothermophilus
brenda
Justesen, J.; Lund, T.; Skou Pedersen, F.; Kjeldgaard, N.O.
The physiology of stringent factor (ATP:GTP 3-diphosphotransferase) in Escherichia coli
Biochimie
68
715-722
1986
Escherichia coli
brenda
Jones, G.H.
Purification and properties of ATP:GTP 3-pyrophosphotransferase (guanosine pentaphosphate synthetase) from Streptomyces antibioticus
J. Bacteriol.
176
1475-1481
1994
Saccharopolyspora erythraea, Streptomyces albus, Streptomyces ambofaciens, Streptomyces antibioticus, Streptomyces anulatus, Streptomyces coelicolor, Streptomyces fradiae, Streptomyces fradiae UC8306, Streptomyces glaucescens, Streptomyces glaucescens ETH 22794, Streptomyces lividans, Streptomyces lividans TK24, Streptomyces parvulus
brenda
Jones, G.H.
Activation of ATP:GTP 3-pyrophosphotransferase (guanosine pentaphosphate synthetase) in Streptomyces antibioticus
J. Bacteriol.
176
1482-1487
1994
Streptomyces antibioticus
brenda
Metzger, S.; Dror, I.B.; Aizenman, E.; Schreiber, G.; Toone, M.; Friesen, J.D.; Cashel, M.; Glaser, G.
The nucleotide sequence and characterization of the relA gene of Escherichia coli
J. Biol. Chem.
263
15699-15704
1988
Escherichia coli
brenda
Jones, G.H.; Bibb, M.J.
Guanosine pentaphosphate synthetase from Streptomyces antibioticus is also a polynucleotide phosphorylase
J. Bacteriol.
178
4281-4288
1996
Streptomyces antibioticus (Q53597), Streptomyces antibioticus
brenda
Avarbock, A.; Avarbock, D.; Teh, J.S.; Buckstein, M.; Wang, Z.m.; Rubin, H.
Functional Regulation of the Opposing (p)ppGpp Synthetase/Hydrolase Activities of RelMtb from Mycobacterium tuberculosis
Biochemistry
44
9913-9923
2005
Mycobacterium tuberculosis
brenda
Hogg, T.; Mechold, U.; Malke, H.; Cashel, M.; Hilgenfeld, R.
Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected]
Cell
117
57-68
2004
Streptococcus dysgalactiae
brenda
Knutsson Jenvert, R.M.; Holmberg Schiavone, L.
Characterization of the tRNA and ribosome-dependent pppGpp-synthesis by recombinant stringent factor from Escherichia coli
FEBS J.
272
685-695
2005
Escherichia coli, Escherichia coli MRE 600
brenda
Gruendling, A.; Missiakas, D.M.; Schneewind, O.
Staphylococcus aureus mutants with increased lysostaphin resistance
J. Bacteriol.
188
6286-6297
2006
Staphylococcus aureus
brenda
Payoe, R.; Fahlman, R.
Dependence of rela-mediated (p)ppGpp formation on tRNA identity
Biochemistry
50
3075-3083
2011
Escherichia coli
brenda
Murdeshwar, M.S.; Chatterji, D.
MS_RHII-RSD, a dual-function RNase HII-(p)ppGpp synthetase from Mycobacterium smegmatis
J. Bacteriol.
194
4003-4014
2012
Mycolicibacterium smegmatis, Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
brenda
Wilkinson, R.C.; Batten, L.E.; Wells, N.J.; Oyston, P.C.; Roach, P.L.
Biochemical studies on Francisella tularensis RelA in (p)ppGpp biosynthesis
Biosci. Rep.
35
0000
2015
Francisella tularensis subsp. tularensis (Q5NEV0)
brenda
Weiss, L.A.; Stallings, C.L.
Essential roles for Mycobacterium tuberculosis Rel beyond the production of (p)ppGpp
J. Bacteriol.
195
5629-5638
2013
Mycobacterium tuberculosis, Mycobacterium tuberculosis (P9WHG9), Mycobacterium tuberculosis ATCC 25618 (P9WHG9)
brenda
Kriel, A.; Brinsmade, S.R.; Tse, J.L.; Tehranchi, A.K.; Bittner, A.N.; Sonenshein, A.L.; Wang, J.D.
GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes
J. Bacteriol.
196
189-201
2014
Bacillus subtilis 168 (O31611), Bacillus subtilis 168 (O54408), Bacillus subtilis 168 (P39583), Bacillus subtilis, Bacillus subtilis (O31611), Bacillus subtilis (O54408), Bacillus subtilis (P39583)
brenda
Steinchen, W.; Schuhmacher, J.S.; Altegoer, F.; Fage, C.D.; Srinivasan, V.; Linne, U.; Marahiel, M.A.; Bange, G.
Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone
Proc. Natl. Acad. Sci. USA
112
13348-13353
2015
Bacillus subtilis 168 (O31611), Bacillus subtilis, Bacillus subtilis (O31611)
brenda
Fernandez-Coll, L.; Cashel, M.
Contributions of SpoT hydrolase, SpoT synthetase, and RelA synthetase to carbon source diauxic growth transitions in Escherichia coli
Front. Microbiol.
9
1802
2018
Escherichia coli (P0AG24)
brenda
Honoki, R.; Ono, S.; Oikawa, A.; Saito, K.; Masuda, S.
Significance of accumulation of the alarmone (p)ppGpp in chloroplasts for controlling photosynthesis and metabolite balance during nitrogen starvation in Arabidopsis
Photosyn. Res.
135
299-308
2018
Arabidopsis thaliana (Q9SYH1)
brenda
Gratani, F.; Horvatek, P.; Geiger, T.; Borisova, M.; Mayer, C.; Grin, I.; Wagner, S.; Steinchen, W.; Bange, G.; Velic, A.; Macek, B.; Wolz, C.
Regulation of the opposing (p)ppGpp synthetase and hydrolase activities in a bifunctional RelA/SpoT homologue from Staphylococcus aureus
PLoS Genet.
14
e1007514
2018
Staphylococcus aureus, Staphylococcus aureus (W8U368)
brenda
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