Information on EC 2.7.1.165 - glycerate 2-kinase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
2.7.1.165
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RECOMMENDED NAME
GeneOntology No.
glycerate 2-kinase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + D-glycerate = ADP + 2-phospho-D-glycerate
show the reaction diagram
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
2-O-alpha-mannosyl-D-glycerate degradation
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D-galactarate degradation I
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D-glucarate degradation I
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Entner-Doudoroff pathway II (non-phosphorylative)
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formaldehyde assimilation I (serine pathway)
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glycolate and glyoxylate degradation I
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degradation of sugar acids
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Entner Doudoroff pathway
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serine metabolism
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Pentose phosphate pathway
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Glycine, serine and threonine metabolism
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Glycerolipid metabolism
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Glyoxylate and dicarboxylate metabolism
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Methane metabolism
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Metabolic pathways
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Microbial metabolism in diverse environments
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Biosynthesis of antibiotics
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SYSTEMATIC NAME
IUBMB Comments
ATP:(R)-glycerate 2-phosphotransferase
A key enzyme in the nonphosphorylative Entner-Doudoroff pathway in archaea [1,2]. In the bacterium Hyphomicrobium methylovorum GM2 the enzyme is involved in formaldehyde assimilation I (serine pathway) [5]. In Escherichia coli the enzyme is involved in D-glucarate/D-galactarate degradation [6]. The enzyme requires a divalent metal ion [1].
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase
metabolism
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP + (R)-glycerate
AMP + 2-phospho-(R)-glycerate
show the reaction diagram
ADP + (R)-glycerate
AMP + 3-phospho-(R)-glycerate
show the reaction diagram
at 32% of the activity with ATP
-
-
?
ADP + D-glycerate
AMP + 2-phospho-D-glycerate
show the reaction diagram
76% activity compared to GTP
-
-
?
AMP + (R)-glycerate
adenosine + 2-phospho-(R)-glycerate
show the reaction diagram
54% of the activity with GTP
-
-
?
AMP + D-glycerate
adenosine + 2-phospho-D-glycerate
show the reaction diagram
54% activity compared to GTP
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
show the reaction diagram
ATP + (R)-glycerate
ADP + 3-phospho-(R)-glycerate
show the reaction diagram
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
show the reaction diagram
CTP + (R)-glycerate
CDP + 2-phospho-(R)-glycerate
show the reaction diagram
CTP + (R)-glycerate
CDP + 3-phospho-(R)-glycerate
show the reaction diagram
CTP + D-glycerate
CDP + 2-phospho-D-glycerate
show the reaction diagram
87% activity compared to GTP
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-
?
diphosphate + (R)-glycerate
phosphate + 2-phospho-(R)-glycerate
show the reaction diagram
diphosphate + (R)-glycerate
phosphate + 3-phospho-(R)-glycerate
show the reaction diagram
at 112% of the activity with ATP
-
-
?
diphosphate + D-glycerate
phosphate + 2-phospho-D-glycerate
show the reaction diagram
63% activity compared to GTP
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-
?
GTP + (R)-glycerate
GDP + 2-phospho-(R)-glycerate
show the reaction diagram
GTP + (R)-glycerate
GDP + 3-phospho-(R)-glycerate
show the reaction diagram
GTP + D-glycerate
GDP + 2-phospho-D-glycerate
show the reaction diagram
100% activity towards GTP
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-
?
TTP + (R)-glycerate
TDP + 2-phospho-(R)-glycerate
show the reaction diagram
16% of the activity with ATP
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-
?
UTP + (R)-glycerate
UDP + 2-phospho-(R)-glycerate
show the reaction diagram
UTP + (R)-glycerate
UDP + 3-phospho-(R)-glycerate
show the reaction diagram
UTP + D-glycerate
UDP + 2-phospho-D-glycerate
show the reaction diagram
81% activity compared to GTP
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?
additional information
?
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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 + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
show the reaction diagram
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Li+
2.28fold increase of activity at 50 mM; 50 mM, 2.3fold activation
Na+
3.49fold increase of activity at 50 mM; 50 mM, 3.5fold activation
Sr2+
divalent metal ion required, Sr2+ (10 mM) shows 79% of the activity compared to Mg2+
Zn2+
divalent metal ion required, Zn2+ (10 mM) shows 84% of the activity compared to Mg2+
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(R)-glycerate
2,3-diphospho-D-glycerate
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2-propanol
10% v/v, less than 65% inhibition; less than 65% activity in the presence of 10% (v/v)
3-phosphoglycerate
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ATP
; weak substrate inhibition
CuCl2
D-glycerate
substrate inhibition; substrate inhibition at glycerate concentrations higher than 2 mM at 80C, above 2 mM at 70C and 5 mM at 65C
ethanol
10% v/v, less than 65% inhibition; less than 65% activity in the presence of 10% (v/v)
guanidine hydrochloride
85% residual activity at 1 M guanidine hydrochloride
HgCl2
Hydroxypyruvate
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Mn2+
93% activity in the presence of 10 mM Mn2+ compared to Mg2+
n-butanol
10% v/v, less than 65% inhibition; less than 65% activity in the presence of 10% (v/v)
Ni2+
68% activity in the presence of 10 mM Ni2+ compared to Mg2+
p-chloromercuribenzoate
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Phenylmethylsulfonylfluoride
less than 30% residual activity at 10 mM
PMSF
10 mM, more than 70% inhibition
SDS
10 mM, more than 60% inhibition; less than 40% residual activity at 10 mM
Sodium fluoride
65% residual activity at 1 M sodium fluoride
Sr2+
79% activity in the presence of 10 mM Sr2+ compared to Mg2+
Zn2+
84% activity in the presence of 10 mM Zn2+ compared to Mg2+
additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dithiothreitol
activity is 10fold elevated by addition of 5 mM dithiothreitol to the enzyme assay
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.02 - 0.56
(R)-glycerate
0.03 - 0.5
ATP
0.043 - 0.56
D-glycerate
0.044
glycerate
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.5 - 360
(R)-glycerate
3.1 - 500.6
ATP
3.6 - 533.3
D-glycerate
489.2
glycerate
Pyrococcus horikoshii
O58231
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
61
ATP
in 100 mM HEPES/KOH, pH 7.0, at 37C; pH 6.5, 80C
0.1
D-glycerate
in 100 mM HEPES/KOH, pH 7.0, at 37C; pH 6.5, 80C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.07
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cell extract, at 50C
0.16
crude extract, using (R)-glycerate as a substrate, at pH 8.0
118
after 747fold purification, using (R)-glycerate as a substrate, at pH 8.0; pH 8.0, 55C
358
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after 5114fold purification, at 50C
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 - 9
pH 3: about 85% of maximal activity, pH 9.0: about 50% of maximal activity
6 - 10
50% of maximal activity at pH 6.0 and 10.0
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20 - 85
20C: about 40% of maximal activity, 85C: about 50% of maximal activity
30 - 50
strong activity at 30-50C
45 - 100
45C: optimum, 100C: about 50% of maximal activity
50 - 90
50C: 15% of maximal activity, 70C: 55% of maximal activity, 90C: maximal activity
70 - 100
; 70C: about 60% of maximal activity, 100C: about 85% of maximal activity
70 - 80
activity decreases rapidly at temperatures above 80C, but slowly at temperatures below 70C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41000 - 48000
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gel filtration
42400
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calculated from amino acid sequence
44000
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SDS-PAGE, denatured enzyme
45000
SDS-PAGE, denatured enzyme
45820
calculated from amino acid sequence
47400
calculated from amino acid sequence
49000
SDS-PAGE, native enzyme
49300
gel filtration; Sephacryl S-200 column gel filtration
50000
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SDS-PAGE, denatured enzyme
80000
gel filtration
90000
gel filtration
93000
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calculated from amino acid sequence
95000
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gel filtration, native enzyme
100000
gel filtration; gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 * 47000, SDS-PAGE; 2 * 50000, gel filtration
homodimer
monomer
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.6 - 8.6
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50% of activity at pH 5.6 and at pH 8.6
673730
6 - 10
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35
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30 min, stable
40
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30 min, 14.3% loss of activity
60
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30 min, 87.3% loss of activity
70
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30 min, 100% loss of activity
70 - 80
exhibits excellent thermal stability at 70C, activity decreases rapidly at temperatures above 80C, but slowly at temperatures below 70C, at temperatures up to 75C, glycerate kinase is stable for over 2 h but at 78C its activity is reduced to less than 50% in one hour, and at 80C its activity diminishes rapidly, with less than 5% of its initial activity remaining after 20 min
70
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at 70C 55% residual activity
75
stable for over 2 h
78
1 h, activity is reduced to less than 50%
80
less than 5% of its initial activity remaining after 20 min
90
12 h, no loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
resistant to the 1 mM guanidine hydrochloride (85% of the original activity) and 1 mM NaF (65% of original activity) relatively stable in 10 mM MnCl2, CoSO4, CaCl2, SrCl2, NiCl2, CuCl2, HgCl2
the enzyme does not require dithiothreitol to retain full activity
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the enzyme retains full activity through at least one freezethaw cycle
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2-propanol
resistant to
DMSO
resistant to
Ethanol
resistant to
n-Butanol
resistant to
urea
resistant to
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C, storage buffer containing 1 mM NaN3, enzyme retains full activity through prolonged storage
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60C, 100 mM Tris-HCl at pH 8.0, 2 h, no loss of activity
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70C, 100 mM Tris-HCl at pH 8.0, 5 min, 50% loss of activity
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75C, 100 mM Tris-HCl (pH 8), over 2 h, no loss of activity
78C, 100 mM Tris-HCl (pH 8), 1 h, 50% loss of activity
80C, 100 mM Tris-HCl (pH 8), 20 min, 95% loss of activity
90C, 50 mM Tris-HCl and 100 mM NaCl buffer (pH 8.0), 12 h, almost no loss of activity
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
; DEAE Sepharose column chromatography, Q-Sepharose column chromatography, Phenyl-Sepharose column chromatography, and Affi-gel blue column chromatography
; UNO Q-12 column chromatography and Superdex 200 gel filtration
Ni-NTA column chromatography; recombinant enzyme
nickel affinity chromatography, HiTrap Q ion exchange chromatography, and SephacrylTM S-200 HR gel filtration
Q-sepharose column chromatography, phenyl sepharose column chromatography, and HiLoad 26/60 Superdex 200 prep grade gel filtration
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Resource Phenyl column chromatography, Superdex 200 HiLoad 16/60 column gel filtration, and UNO-Q1 column chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
; expressed in Escherichia coli
expressed in Escherichia coli BL21 (DE3) cells
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expressed in Escherichia coli BL21(DE3)-RIL cells; expression in Escherichia coli
expressed in Escherichia coli; expressed in Escherichia coli BL21(DE3) cells
expressed in HEK-293 cells
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expression in Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
F483S
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the mutant shows loss of enzyme activity. The mutation leads to D-glyceric acidemia
F493C
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the mutant shows loss of enzyme activity. The mutation leads to D-glyceric acidemia
L510C
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the mutant shows loss of enzyme activity. The mutation leads to D-glyceric acidemia
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
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synthesis of 2-phospho-D-glycerate, quickly, inexpensively
Show AA Sequence (169 entries)
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