Information on EC 2.7.6.5 - GTP diphosphokinase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
2.7.6.5
-
RECOMMENDED NAME
GeneOntology No.
GTP diphosphokinase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
GDP can also act as acceptor
-
-
-
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
bifunctional enzyme, additionally has polynucleotide phosphorylase activities
Q53597, -
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
diphosphate transfer
-
-
-
-
diphosphate transfer
-
-
diphosphate transfer
-
-
diphosphate transfer
-
-
diphosphate transfer
Escherichia coli MRE 600
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
ppGpp biosynthesis
-
Purine metabolism
-
SYSTEMATIC NAME
IUBMB Comments
ATP:GTP 3'-diphosphotransferase
GDP can also act as acceptor.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
(p)ppGpp synthetase
-
-
(p)ppGpp synthetase
-
-
(p)ppGpp synthetase
Mycobacterium smegmatis mc2155
-
-
-
(p)ppGpp synthetase I
-
-
-
-
(p)ppGpp synthetase II
-
-
-
-
(p)ppGpp synthetase/hydrolase
-
-
ATP-GTP 3'-diphosphotransferase
-
-
-
-
ATP:GTP pyrophosphoryl transferase
-
-
ATP:GTP pyrophosphoryl transferase
Escherichia coli MRE 600
-
-
-
GPSI
-
-
-
-
GPSII
-
-
-
-
GTP pyrophosphokinase
-
-
-
-
GTP pyrophosphokinase
-
-
guanosine 3',5'-polyphosphate synthase
-
-
-
-
guanosine 3',5'-polyphosphate synthetase
-
-
-
-
guanosine 5',3'-polyphosphate synthetase
-
-
-
-
guanosine pentaphosphate synthetase
-
-
-
-
Rel
Mycobacterium smegmatis mc2155
-
-
-
Rel/Spo protein
-
-
RelMtb protein
-
-
SF
Escherichia coli MRE 600
-
-
-
stringent factor
-
-
-
-
stringent factor
-
-
stringent factor
Escherichia coli MRE 600
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
63690-89-1
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
MRE 600
-
-
Manually annotated by BRENDA team
Escherichia coli MRE 600
MRE 600
-
-
Manually annotated by BRENDA team
2 different enzymes: (p)ppGpp synthetase I, (p)ppGpp synthetase II
-
-
Manually annotated by BRENDA team
Mycobacterium smegmatis mc2155
-
-
-
Manually annotated by BRENDA team
subsp. equisimilis
-
-
Manually annotated by BRENDA team
ATCC 21828
-
-
Manually annotated by BRENDA team
2 enzyme forms: GPS I
-
-
Manually annotated by BRENDA team
2 enzyme forms: GPS I; GPS II
-
-
Manually annotated by BRENDA team
ATCC 11523
-
-
Manually annotated by BRENDA team
Streptomyces coelicolor A3
A3
-
-
Manually annotated by BRENDA team
Streptomyces fradiae UC8306
UC8306
-
-
Manually annotated by BRENDA team
Streptomyces glaucescens ETH 22794
ETH 22794
-
-
Manually annotated by BRENDA team
ATCC 12434
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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'-diphosphate 5'-diphosphate
show the reaction diagram
-
preferred substrate
-
-
?
ATP + GDP
AMP + guanosine 3'-diphosphate 5'-diphosphate
show the reaction diagram
-
preferred substrate
i.e ppGpp
?
ATP + GDP
AMP + guanosine 3,5-bis-diphosphate
show the reaction diagram
Mycobacterium smegmatis, Mycobacterium smegmatis mc2155
-
the enzyme utilizes GDP less efficiently than GTP
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
-
-
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
-
-, ?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
Q53597, -
-
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
-
i.e. pppGpp
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
-
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
show the reaction diagram
Mycobacterium smegmatis, Mycobacterium smegmatis mc2155
-
the enzyme uses GTP approximately twice as well as GDP
-
-
?
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
show the reaction diagram
Streptomyces coelicolor A3, Streptomyces fradiae UC8306, Streptomyces glaucescens ETH 22794, Streptomyces lividans TK24
-
-
-
?
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
-
-
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
-
-
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
-
bifunctional enzyme with synthetase and hydrolase activities
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
Escherichia coli MRE 600
-
-
-
-
r
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
-
-
-
-
?
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
?
-
-
(p)ppGpp synthetase II is responsible for (p)ppGpp accumulation during carbon source downshift
-
-
-
additional information
?
-
-
responsible for the synthesis of guanosine 3',5'-bisdiphosphate during stringent response to amino acid starvation
-
-
-
additional information
?
-
Mycobacterium smegmatis, Mycobacterium smegmatis mc2155
-
the enzyme also possesses a potent Mn2+-dependent guanosine tetraphosphate hydrolysis activity, with complete hydrolysis to GDP and diphosphate
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + GTP
AMP + guanosine 3'-diphosphate 5'-triphosphate
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
-
-
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
-
-
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
-
bifunctional enzyme with synthetase and hydrolase activities
-
-
r
ATP + GTP
AMP + guanosine 5'-triphosphate 3'-diphosphate
show the reaction diagram
Escherichia coli MRE 600
-
-
-
-
r
additional information
?
-
-
(p)ppGpp synthetase II is responsible for (p)ppGpp accumulation during carbon source downshift
-
-
-
additional information
?
-
-
responsible for the synthesis of guanosine 3',5'-bisdiphosphate during stringent response to amino acid starvation
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Mg2+
-
required as a counter-ion for the nucleoside substrate, excess of Mg2+ is inhibitory
Mg2+
-
the optimal concentration for pppGpp synthesis is approximately equal to the total concentration of nucleotide substrates([ATP] + [GTP])
Mg2+
-
essential for activation, the enzyme has a single Mg2+ binding site
Mg2+
-
the magnesium concentration also affects the binding states of the tRNAs on the ribosome
Mg2+
-
the enzyme exploits a single Mg2+ ion to catalyze guanosine 3'-diphosphate 5'-triphosphate synthesis
Mn2+
-
can partially replace Mg2+ in activation
Mn2+
-
the optimal concentration for pppGpp synthesis is approximately one-half of the total concentration of nucleotide substrates([ATP] + [GTP])
Mn2+
-
necessary cofactor at the hydrolase active site
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
adenosine 5'-(beta,gamma-Imino)triphosphate
-
-
alpha,beta-methylene-ATP
-
-
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
micrococcin
-
ribosome-dependent activity
tetracycline
-
not (p)ppGpp synthetase II
tetracycline
-
endogenous diphoyphoryl transferase activity; ribosome-dependent activity
Thiostrepton
-
not (p)ppGpp synthetase II
Thiostrepton
-
ribosome-dependent activity
viomycin
-
ribosome-dependent activity
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
dCDP
Q53597, -
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%
mRNA
-
(p)ppGpp synthetase II does not
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
tRNA
-
uncharged or charged, stimulation, level of stimulation is greater in presence of RNA and poly(U) together than with either RNA alone
Trypsin
-
incubation with low levels of trypsin activates
-
unacylated tRNA
-
in the ribosomal amino-acyl site (A-site)
-
methanol
-
maximal stimulation of GPSI by 20% v/v
additional information
-
(p)ppGpp synthetase II does not
-
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
-
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
-
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
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.05
-
ATP
-
synthetase II, pH 7.8, 37C
0.62
-
ATP
-
cosubstrate GDP, pH 8.1, 30C
0.71
-
ATP
-
cosubstrate GTP, pH 8.1, 30C
2
-
ATP
-
synthetase I, pH 7.8, 37C
0.14
-
GDP
-
30C, pH 8.1
1.532
-
GDP
-
in 50 mM HEPES, pH 7.5, at 37C
0.33
-
GTP
-
full length enzyme + tRNA + ribosomes + poly(U)
0.67
-
GTP
-
fragment 1-394 monomer; fragment 1-394 + tRNA; fragment 1-394 + tRNA + ribosomes + poly(U)
0.7
-
GTP
-
full length enzyme + tRNA
0.77
-
GTP
-
30C, pH 8.1
0.78
-
GTP
-
fragment 87-394; fragment 87-394 + tRNA; fragment 87-394 + tRNA + ribosomes + poly(U)
1.163
-
GTP
-
in 50 mM HEPES, pH 7.5, at 37C
1.36
-
GTP
-
full length enzyme
additional information
-
additional information
-
-
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
73
-
GDP
-
in 50 mM HEPES, pH 7.5, at 37C
0.4
-
GTP
-
full length enzyme; full length enzyme + tRNA
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)
8.4
-
GTP
-
full length enzyme + tRNA + ribosomes + poly(U)
127
-
GTP
-
in 50 mM HEPES, pH 7.5, at 37C
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
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
-
-
-
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
8.1
-
-
calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
Streptomyces coelicolor A3, Streptomyces fradiae UC8306, Streptomyces glaucescens ETH 22794, Streptomyces lividans TK24
-
-
-
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / TLS)
Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / TLS)
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
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
240000
-
-
full-length enzyme, gel filtration
245000
-
-
full-length enzyme, calculated from amino acid sequence
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
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 ACCESSION NO.
LITERATURE
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)
-
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
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
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
affinity-chromatography and precipitation
-
HiTrap column chromatography
-
Ni-NTA column chromatography, and gel filtration
-
the catalytic fragment RelSeq 1-385
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli BL21 cells
-
expression in Escherichia coli BL21(DE3)
-
expressed in Escherichia coli BL21(DE3) cells
-
expression in Escherichia coli and Mycobacterium smegmatis
-
expression of the N-terminal catalytic fragment (residues 1-385) in Escherichia coli BL21
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
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
-
loss of synthetic activity and retention of hydrolysis
D264G
-
eliminates detectable synthetase activity without appreciably altering the hydrolase activity
E323Q
-
eliminates detectable synthetase activity without appreciably altering the hydrolase activity
H80A
-
loss of hydrolytic activity with retention of synthesis
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
Renatured/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
the purified enzyme is renatured by stepwise dialysis in buffers containing sequentially decreasing concentrations of urea (50mM Tris-HCl, pH 7.9 at 4C, 150 mM NaCl, 100 mM imidazole, and 4 M, 2 M, and 0 M urea, in that order)
-
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
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