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Information on EC 2.7.1.165 - glycerate 2-kinase
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2.7.1.165 glycerate 2-kinaseIUBMB Comments
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) . In Escherichia coli the enzyme is involved in D-glucarate/D-galactarate degradation . The enzyme requires a divalent metal ion .
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Word Map
- 2.7.1.165
-
thermoacidophilic
- synthesis
-
entner-doudoroff
-
non-phosphorylative
-
homodimeric
-
picrophilus
- thermoplasma
- sulfolobus
- 2-keto-3-deoxygluconate
- torridus
- archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
glycerate kinase (2-phosphoglycerate forming), sso-gk, tm1585, glycerate 2-kinase, class ii glycerate kinase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
class II glycerate kinase
D-glycerate 2-kinase
garK
GCK
glycerate kinase
GLYK
Sso-GK
SSO0666
TM1585
TM_1585
additional information
-
member of the multi-organism fragment with rich leucine kinase family
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + D-glycerate = ADP + 2-phospho-D-glycerate
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
KEGG
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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].
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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
ADP + (R)-glycerate
AMP + 3-phospho-(R)-glycerate
at 32% of the activity with ATP
-
-
?
ADP + D-glycerate
AMP + 2-phospho-D-glycerate
76% activity compared to GTP
-
-
?
AMP + (R)-glycerate
adenosine + 2-phospho-(R)-glycerate
54% of the activity with GTP
-
-
?
AMP + D-glycerate
adenosine + 2-phospho-D-glycerate
54% activity compared to GTP
-
-
?
CTP + D-glycerate
CDP + 2-phospho-D-glycerate
87% activity compared to GTP
-
-
?
diphosphate + (R)-glycerate
phosphate + 3-phospho-(R)-glycerate
at 112% of the activity with ATP
-
-
?
diphosphate + D-glycerate
phosphate + 2-phospho-D-glycerate
63% activity compared to GTP
-
-
?
GTP + D-glycerate
GDP + 2-phospho-D-glycerate
100% activity towards GTP
-
-
?
TTP + (R)-glycerate
TDP + 2-phospho-(R)-glycerate
16% of the activity with ATP
-
-
?
UTP + D-glycerate
UDP + 2-phospho-D-glycerate
81% activity compared to GTP
-
-
?
ADP + (R)-glycerate
AMP + 2-phospho-(R)-glycerate
32% of the activity with ATP
-
-
?
ADP + (R)-glycerate
AMP + 2-phospho-(R)-glycerate
76% of the activity with GTP
-
-
?
ADP + (R)-glycerate
AMP + 2-phospho-(R)-glycerate
76% of the activity with GTP
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
-
enzymes in the (D)-glucarate/galactarate catabolic pathway
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
-
no activity with (S)-glycerate
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
-
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
key enzyme in the Entner-Doudoroff pathway in archaea
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
92% of the activity with GTP
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
key enzyme in the Entner-Doudoroff pathway in archaea
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
92% of the activity with GTP
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
enzyme of the branched Entner-Doudoroff pathway
-
-
?
ATP + (R)-glycerate
ADP + 3-phospho-(R)-glycerate
-
activity towards L-glycerate is 13% of that towards D-glycerate
2-phosphoglycerate
ir
ATP + (R)-glycerate
ADP + 3-phospho-(R)-glycerate
-
-
2-phosphoglycerate
?
ATP + (R)-glycerate
ADP + 3-phospho-(R)-glycerate
-
-
2-phosphoglycerate
?
ATP + D-glycerate
ADP + 2-phospho-(R)-glycerate
the enzyme shows selectivity and excellent enantioselectivity towards phosphorylation of the D-enantiomer of glyceric acid
-
-
?
ATP + D-glycerate
ADP + 2-phospho-(R)-glycerate
-
-
-
?
ATP + D-glycerate
ADP + 2-phospho-(R)-glycerate
the enzyme shows selectivity and excellent enantioselectivity towards phosphorylation of the D-enantiomer of glyceric acid
-
-
?
ATP + D-glycerate
ADP + 2-phospho-(R)-glycerate
the enzyme shows selectivity and excellent enantioselectivity towards phosphorylation of the D-enantiomer of glyceric acid
-
-
?
ATP + D-glycerate
ADP + 2-phospho-(R)-glycerate
the enzyme shows selectivity and excellent enantioselectivity towards phosphorylation of the D-enantiomer of glyceric acid
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
specific substrate
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
a key enzyme in the nonphosphorylative Entner-Doudoroff pathway in archaea. The glycerate kinase, with its unusual regulatory properties, seems to play a major role in controlling the flux between the glycolytic nonphosphorylative Entner-Doudoroff and the glycolytic/gluconeogenetic semiphosphorylative Entner-Doudoroff pathway
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
the enzyme is specific for D-glycerate. The enzyme shows cooperativity by D-glycerate and ATP. A good fit achieved from the kinetic model to the experimental data suggests a mechanism where two glycerate molecules bind to glycerate kinase and are converted to product, while a third binding site appears to be inhibitory. The model suggests that the inhibition appears to be due to the formation of an additional complex with very low activity at 80°C
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
specific substrate
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
a key enzyme in the nonphosphorylative Entner-Doudoroff pathway in archaea. The glycerate kinase, with its unusual regulatory properties, seems to play a major role in controlling the flux between the glycolytic nonphosphorylative Entner-Doudoroff and the glycolytic/gluconeogenetic semiphosphorylative Entner-Doudoroff pathway
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
the enzyme is specific for D-glycerate. The enzyme shows cooperativity by D-glycerate and ATP. A good fit achieved from the kinetic model to the experimental data suggests a mechanism where two glycerate molecules bind to glycerate kinase and are converted to product, while a third binding site appears to be inhibitory. The model suggests that the inhibition appears to be due to the formation of an additional complex with very low activity at 80°C
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
92% activity compared to GTP
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
no activity with DL-glyceraldehyde, 2-phospho-D-glycerate, 3-phospho-D-glycerate or L-tartrate. Activity with D-gluconate or glycerol at 5% of the activity compared to D-glycerate. Specificity for ATP as a phosphate donor. GTP, CTP, and UTP exhibit 0~4% of the activity of ATP
-
-
?
CTP + (R)-glycerate
CDP + 2-phospho-(R)-glycerate
73% of the activity with ATP
-
-
?
CTP + (R)-glycerate
CDP + 2-phospho-(R)-glycerate
87% of the activity with GTP
-
-
?
CTP + (R)-glycerate
CDP + 2-phospho-(R)-glycerate
87% of the activity with GTP
-
-
?
CTP + (R)-glycerate
CDP + 2-phospho-(R)-glycerate
16% of the activity with ATP
-
-
?
CTP + (R)-glycerate
CDP + 3-phospho-(R)-glycerate
-
at 59% of the activity with ATP
-
-
?
CTP + (R)-glycerate
CDP + 3-phospho-(R)-glycerate
at 73% of the activity with ATP
-
-
?
diphosphate + (R)-glycerate
phosphate + 2-phospho-(R)-glycerate
112% of the activity with ATP
-
-
?
diphosphate + (R)-glycerate
phosphate + 2-phospho-(R)-glycerate
63% of the activity with ATP
-
-
?
diphosphate + (R)-glycerate
phosphate + 2-phospho-(R)-glycerate
63% of the activity with ATP
-
-
?
GTP + (R)-glycerate
GDP + 2-phospho-(R)-glycerate
64% of the activity with ATP
-
-
?
GTP + (R)-glycerate
GDP + 2-phospho-(R)-glycerate
20% of the activity with ATP
-
-
?
GTP + (R)-glycerate
GDP + 3-phospho-(R)-glycerate
-
at 59% of the activity with ATP
-
-
?
GTP + (R)-glycerate
GDP + 3-phospho-(R)-glycerate
at 64% of the activity with ATP
-
-
?
UTP + (R)-glycerate
UDP + 2-phospho-(R)-glycerate
29% of the activity with ATP
-
-
?
UTP + (R)-glycerate
UDP + 2-phospho-(R)-glycerate
81% of the activity with GTP
-
-
?
UTP + (R)-glycerate
UDP + 2-phospho-(R)-glycerate
10% of the activity with ATP
-
-
?
UTP + (R)-glycerate
UDP + 3-phospho-(R)-glycerate
-
at 64% of the activity with ATP
-
-
?
UTP + (R)-glycerate
UDP + 3-phospho-(R)-glycerate
at 29% of the activity with ATP
-
-
?
additional information
?
-
-
the enzyme shows highest activity with D-glycerate (100%), and lower activity (34%) with L-glycerate
-
-
?
additional information
?
-
-
GTP, CTP, UTP, D-glucose, D-gluconate, glycerol, D-fructose, DL-glyceraldehyde, D-ribose, D-xylose, 2-phospho-D-glycerate, 3-phospho-D-glycerate, and L-tartrate are no substrates
-
-
?
additional information
?
-
GTP, CTP, UTP, D-glucose, D-gluconate, glycerol, D-fructose, DL-glyceraldehyde, D-ribose, D-xylose, 2-phospho-D-glycerate, 3-phospho-D-glycerate, and L-tartrate are no substrates
-
-
?
additional information
?
-
-
ATP can be partially replaced by GTP, CTP, TTP and UTP (16%, 20%, 16%, and 10% activity, respectively)
-
-
?
additional information
?
-
-
L-glycerate, galactonate, gluconate, malate, pyruvate, lactate, glyceraldehyde, glycerol, serine, 3-phosphoglycerate, ADP, diphosphate, polyphosphate, and glyceraldehyde 3-phosphate are no substrates
-
-
?
additional information
?
-
no activity is observed with ADP, diphosphate and polyphosphates
-
-
?
additional information
?
-
biocatalytic phosphorylations catalyzed by recombinant glycerate-2-kinase are detected with quantitative 31P NMR spectroscopy using a phosphoenolpyruvate (PEP)/pyruvate kinase system for ATP regeneration, starting with racemic and the enantiopure D- and L-glycerate as substrate. Nearly 100% conversion of D-glycerate to D-glycerate-2-phosphate is observed. No activity with pure L-glycerate as substrate, DL-glycerate gives a 50% conversion with excellent enantioselectivity. Optimization of the reaction system for the biocatalytic phosphorylation of D-glyceric acid, upscaling, overview
-
-
-
additional information
?
-
biocatalytic phosphorylations catalyzed by recombinant glycerate-2-kinase are detected with quantitative 31P NMR spectroscopy using a phosphoenolpyruvate (PEP)/pyruvate kinase system for ATP regeneration, starting with racemic and the enantiopure D- and L-glycerate as substrate. Nearly 100% conversion of D-glycerate to D-glycerate-2-phosphate is observed. No activity with pure L-glycerate as substrate, DL-glycerate gives a 50% conversion with excellent enantioselectivity. Optimization of the reaction system for the biocatalytic phosphorylation of D-glyceric acid, upscaling, overview
-
-
-
additional information
?
-
biocatalytic phosphorylations catalyzed by recombinant glycerate-2-kinase are detected with quantitative 31P NMR spectroscopy using a phosphoenolpyruvate (PEP)/pyruvate kinase system for ATP regeneration, starting with racemic and the enantiopure D- and L-glycerate as substrate. Nearly 100% conversion of D-glycerate to D-glycerate-2-phosphate is observed. No activity with pure L-glycerate as substrate, DL-glycerate gives a 50% conversion with excellent enantioselectivity. Optimization of the reaction system for the biocatalytic phosphorylation of D-glyceric acid, upscaling, overview
-
-
-
additional information
?
-
biocatalytic phosphorylations catalyzed by recombinant glycerate-2-kinase are detected with quantitative 31P NMR spectroscopy using a phosphoenolpyruvate (PEP)/pyruvate kinase system for ATP regeneration, starting with racemic and the enantiopure D- and L-glycerate as substrate. Nearly 100% conversion of D-glycerate to D-glycerate-2-phosphate is observed. No activity with pure L-glycerate as substrate, DL-glycerate gives a 50% conversion with excellent enantioselectivity. Optimization of the reaction system for the biocatalytic phosphorylation of D-glyceric acid, upscaling, overview
-
-
-
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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 + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
-
enzymes in the (D)-glucarate/galactarate catabolic pathway
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
key enzyme in the Entner-Doudoroff pathway in archaea
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
key enzyme in the Entner-Doudoroff pathway in archaea
-
-
?
ATP + (R)-glycerate
ADP + 2-phospho-(R)-glycerate
enzyme of the branched Entner-Doudoroff pathway
-
-
?
ATP + D-glycerate
ADP + 2-phospho-(R)-glycerate
-
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
a key enzyme in the nonphosphorylative Entner-Doudoroff pathway in archaea. The glycerate kinase, with its unusual regulatory properties, seems to play a major role in controlling the flux between the glycolytic nonphosphorylative Entner-Doudoroff and the glycolytic/gluconeogenetic semiphosphorylative Entner-Doudoroff pathway
-
-
?
ATP + D-glycerate
ADP + 2-phospho-D-glycerate
a key enzyme in the nonphosphorylative Entner-Doudoroff pathway in archaea. The glycerate kinase, with its unusual regulatory properties, seems to play a major role in controlling the flux between the glycolytic nonphosphorylative Entner-Doudoroff and the glycolytic/gluconeogenetic semiphosphorylative Entner-Doudoroff pathway
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Co2+
K+
Li+
Mg2+
Mn2+
Na+
NH4+
Ni2+
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
Ca2+
divalent metal ion required, Ca2+ (10 mM) shows 85% of the activity compared to Mg2+
Co2+
divalent metal ion required, maximal activity in presence of Co2+ or Mg2+ (10 mM)
Co2+
106% activity in the presence of 10 mM Co2+ compared to Mg2+
Co2+
10 mM, can substitute for Mg2+, activity is 8% of the activity activated by Mg2+
Mg2+
no activity is observed in the absence of divalent metal ion and maximal activity is observed in the presence of Mg2+ (10 mM)
Mg2+
divalent metal ion required, maximal activity in presence of Co2+ or Mg2+ (10 mM)
Mn2+
divalent metal ion required, Mn2+ (10 mM) shows 93% of the activity compared to Mg2+
Mn2+
10 mM, can substitute for Mg2+, activity is 10% of the activity activated by Mg2+
Ni2+
divalent metal ion required, Ni2+ (10 mM) shows 68% of the activity compared to Mg2+
additional information
-
Mg2+ can be replaced to some extent by Ni2+ (25%), Mn2+ (11%), and Co2+ (11%)
additional information
-
when Mn2+, Co2+, Ca2+, Sr2+ and Ni2+ is substituted for Mg2+, respectively, Mn2+, Co2+ and Ni2+ show 76, 68 and 11% activity of that for Mg2+
additional information
when Mn2+, Co2+, Ca2+, Sr2+ and Ni2+ is substituted for Mg2+, respectively, Mn2+, Co2+ and Ni2+ show 76, 68 and 11% activity of that for Mg2+
additional information
monovalent metal ions have no effect on the enzyme activity
additional information
-
when divalent metal ions, such as Mn2+, Co2+, Ni2+, Zn2+, Ca2+, and Sr2+, are substituted for Mg2+, the enzyme activity is less than 10% of that obtained in the presence of Mg2+
additional information
when divalent metal ions, such as Mn2+, Co2+, Ni2+, Zn2+, Ca2+, and Sr2+, are substituted for Mg2+, the enzyme activity is less than 10% of that obtained in the presence of Mg2+
additional information
-
Co2+, Mn2+, and Ni2+ (all 5 mM), and Ca2+ (2 mM) can partially replace Mg2+ (56%, 59%, 30% and 15% activity, respectively)
additional information
-
no activity is detected in the presence of Cu2+ and Fe2+ at 0.2, 2, 5 and 20 mM
additional information
no activity is detected in the presence of Cu2+ and Fe2+ at 0.2, 2, 5 and 20 mM, respectively
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-propanol
10% v/v, less than 65% inhibition; less than 65% activity in the presence of 10% (v/v)
D-glycerate
substrate inhibition; substrate inhibition at glycerate concentrations higher than 2 mM at 80°C, above 2 mM at 70°C and 5 mM at 65°C
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
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+
Phenylmethylsulfonylfluoride
less than 30% residual activity at 10 mM
SDS
10 mM, more than 60% inhibition; less than 40% residual activity at 10 mM
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+
(R)-glycerate
-
substrate inhibition is observed at higher glycerate concentrations
(R)-glycerate
substrate inhibition at high glycerate concentrations
ADP
-
1 mM, 91.8% activity loss, at non-saturating concentrations of ATP, competitive inhibition
Ca2+
85% activity in the presence of 10 mM Ca2+ compared to Mg2+
additional information
-
resistant to the urea, ethanol, 2-propanol, n-butanol and DMSO (10% v/v each)
-
additional information
resistant to the urea, ethanol, 2-propanol, n-butanol and DMSO (10% v/v each)
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dithiothreitol
activity is 10fold elevated by addition of 5 mM dithiothreitol to the enzyme assay
additional information
-
50 mM NaN3, 10 mM phenylmethyl sulfonylfluoride, and H2O2 have no obvious effect on the enzymatic activity
-
additional information
50 mM NaN3, 10 mM phenylmethyl sulfonylfluoride, and H2O2 have no obvious effect on the enzymatic activity
-
additional information