Information on EC 2.7.6.5 - GTP diphosphokinase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.7.6.5
-
RECOMMENDED NAME
GeneOntology No.
GTP diphosphokinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
diphosphate transfer
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
ppGpp biosynthesis
-
-
Purine metabolism
-
-
ppGpp biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:GTP 3'-diphosphotransferase
GDP can also act as acceptor.
CAS REGISTRY NUMBER
COMMENTARY hide
63690-89-1
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
ATCC 8185
-
-
Manually annotated by BRENDA team
MRE 600
-
-
Manually annotated by BRENDA team
gene relA or FTT_1508c
UniProt
Manually annotated by BRENDA team
2 different enzymes: (p)ppGpp synthetase I, (p)ppGpp synthetase II
-
-
Manually annotated by BRENDA team
subsp. equisimilis
-
-
Manually annotated by BRENDA team
ATCC 21828
-
-
Manually annotated by BRENDA team
ATCC 15155
-
-
Manually annotated by BRENDA team
ATCC 11523
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-
Manually annotated by BRENDA team
UC8306
-
-
Manually annotated by BRENDA team
ETH 22794
-
-
Manually annotated by BRENDA team
TK24
-
-
Manually annotated by BRENDA team
ATCC 12434
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2'-methyl-ATP + GTP
2'-methyl-AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
-
?
8-bromo-ATP + GTP
8-bromo-AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
-
?
ATP + GDP
AMP + guanosine 3',5'-bis-diphosphate
show the reaction diagram
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
show the reaction diagram
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
ATP + guanosine 5'-tetraphosphate
AMP + guanosine 3'-diphosphate 5'-tetraphosphate
show the reaction diagram
-
-
-
-
?
ATP + ITP
AMP + inosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
-
?
dATP + GTP
dAMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
-
?
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
show the reaction diagram
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
show the reaction diagram
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
guanosine 3'-diphosphate 5'-diphosphate + H2O
GDP + diphosphate
show the reaction diagram
guanosine 3'-diphosphate 5'-triphosphate + H2O
GTP + diphosphate
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
adenosine 5'-(beta,gamma-Imino)triphosphate
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-
alpha,beta-methylene-ATP
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-
micrococcin
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ribosome-dependent activity
tetracycline
Thiostrepton
viomycin
-
ribosome-dependent activity
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
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
-
methanol
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maximal stimulation of GPSI by 20% v/v
tRNA
-
uncharged or charged, stimulation, level of stimulation is greater in presence of RNA and poly(U) together than with either RNA alone
Trypsin
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incubation with low levels of trypsin activates
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unacylated tRNA
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in the ribosomal amino-acyl site (A-site)
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additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05 - 2
ATP
0.14 - 1.532
GDP
0.33 - 1.7
GTP
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
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
73
GDP
Mycobacterium smegmatis
-
in 50 mM HEPES, pH 7.5, at 37°C
0.4 - 127
GTP
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00021
-
mol of PPi/s/mol of enzyme, fragment 1-181
0.027
-
mol of PPi/s/mol of enzyme, fragment 1-394 monomer
0.028
-
mol of PPi/s/mol of enzyme, full length enzyme
0.03
-
mol of PPi/s/mol of enzyme, fragment 1-203
additional information
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-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.1
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calculated from amino acid sequence
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
(p)ppGpp synthetase II
Manually annotated by BRENDA team
-
(p)ppGpp synthetase I
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
47000
-
1 * 47000, GPS II, produced by proteolysis of the larger 88000 MW form, denaturing PAGE, 1 * 88000, GPS I, denaturing PAGE
55000
-
sucrose density gradient centrifugation
74000
-
synthetase II, sucrose density gradient centrifugation
82000
-
full-length enzyme, calculated from OD280
83860
-
deduced from nucleotide sequence
86000
-
synthetase I, sucrose density gradient centrifugation
88000
-
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
148000
about, sequence calculation
240000
-
full-length enzyme, gel filtration
245000
-
full-length enzyme, calculated from amino acid sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
2 * 74000, recombinant His-tagged enzyme, SDS-PAGE
homotetramer
monomer
-
1 * 47000, GPS II, produced by proteolysis of the larger 88000 MW form, denaturing PAGE, 1 * 88000, GPS I, denaturing PAGE
trimer
-
3 * 82000, gel filtration, calculated from OD280
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
-
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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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
affinity-chromatography and precipitation
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HiTrap column chromatography
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Ni-NTA column chromatography, and gel filtration
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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
-
the catalytic fragment RelSeq 1-385
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 cells
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expressed in Escherichia coli BL21(DE3) cells
-
expression in Escherichia coli and Mycobacterium smegmatis
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expression in Escherichia coli BL21(DE3)
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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)
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
CodY-independent activation of transcription of the ywaA operon, overview
the transcription factor CodY represses the ywaA operon, overview
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
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
-
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
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C633A
-
20fold decrease in activity
D632A
-
3.5fold decrease in activity
D81A
-
loss of hydrolytic activity with retention of synthesis
G241E
-
loss of synthetic activity and retention of hydrolysis
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
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 hide
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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