BRENDA - Enzyme Database

Molecular and functional characterization of D-3-phosphoglycerate dehydrogenase in the serine biosynthetic pathway of the hyperthermophilic archaeon Sulfolobus tokodaii

Shimizu, Y.; Sakuraba, H.; Doi, K.; Ohshima, T.; Arch. Biochem. Biophys. 470, 120-128 (2008)

Data extracted from this reference:

Activating Compound
EC Number
Activating Compound
Commentary
Organism
Structure
1.1.1.95
(NH4)2SO4
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
1.1.1.95
K2HPO4
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
Cloned(Commentary)
EC Number
Commentary
Organism
1.1.1.95
expressed in Escherichia coli
Sulfurisphaera tokodaii
General Stability
EC Number
General Stability
Organism
1.1.1.95
enzyme is highly thermostable
Sulfurisphaera tokodaii
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.95
(NH4)2SO4
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
1.1.1.95
3-phosphohydroxypyruvate
product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: 3-phospho-D-glycerate, inhibition pattern: competitive; product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: NAD, inhibition pattern: non-competitive
Sulfurisphaera tokodaii
1.1.1.95
ADP
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 86%
Sulfurisphaera tokodaii
1.1.1.95
AMP
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 75%
Sulfurisphaera tokodaii
1.1.1.95
ATP
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 85%
Sulfurisphaera tokodaii
1.1.1.95
K2HPO4
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction. It appears that the phosphate ion PO43- exerts its inhibitory effect by binding to the free enzyme and NADPH-enzyme complex
Sulfurisphaera tokodaii
1.1.1.95
additional information
unlike the Escherichia coli PGDH no inhibition by L-serine
Sulfurisphaera tokodaii
1.1.1.95
NADH
product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: 3-phospho-D-glycerate, inhibition pattern: non-competitive; product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: NAD, inhibition pattern: competitive
Sulfurisphaera tokodaii
1.1.1.95
ZnCl2
inhibitory effect on 3-phosphohydroxypyruvate reduction, remaining activity: 29%
Sulfurisphaera tokodaii
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.95
0.0013
-
NADH
value for 3-phosphohydroxypyruvate reduction using NADH as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.0096
-
3-phosphohydroxypyruvate
value for 3-phosphohydroxypyruvate reduction using NADH as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.02
-
NADPH
value for 3-phosphohydroxypyruvate reduction using NADPH as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.033
-
3-phospho-D-glycerate
value for 3-phospho-D-glycerate oxidation using NAD+ as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.04
-
NAD+
value for 3-phospho-D-glycerate oxidation
Sulfurisphaera tokodaii
1.1.1.95
0.12
-
3-phosphohydroxypyruvate
value for 3-phosphohydroxypyruvate reduction using NADPH as a cofactor
Sulfurisphaera tokodaii
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.95
35000
-
SDS-PAGE
Sulfurisphaera tokodaii
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.95
Sulfurisphaera tokodaii
-
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.95
using a butyl Sepharose 4 Fast Flow column and a Superdex 200 gel filtration column. During purification an unexpected decline in enzyme activity is observed if the enzyme is stored in plastic tubes, but not in glass ones
Sulfurisphaera tokodaii
Specific Activity [micromol/min/mg]
EC Number
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
1.1.1.95
additional information
-
during purification an unexpected decline in enzyme activity is observed if the enzyme is stored in plastic tubes, but not in glass ones
Sulfurisphaera tokodaii
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.95
2-phospho-D-glycerate + NAD+
activity relative to 3-phospho-D-glycerate: 47%
684698
Sulfurisphaera tokodaii
2-phosphohydroxypyruvate + NADH + H+
-
-
-
?
1.1.1.95
3-phospho-D-glycerate + NAD+
highest activity
684698
Sulfurisphaera tokodaii
3-phosphohydroxypyruvate + NADH + H+
-
-
-
r
1.1.1.95
3-phospho-D-glycerate + NADP+
-
684698
Sulfurisphaera tokodaii
3-phosphohydroxypyruvate + NADPH + H+
-
-
-
r
1.1.1.95
DL-glyceraldehyde 3-phosphate + NAD+
activity relative to 3-phospho-D-glycerate: 9%
684698
Sulfurisphaera tokodaii
?
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.95
homodimer
gel filtration
Sulfurisphaera tokodaii
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.95
50
-
assay at
Sulfurisphaera tokodaii
1.1.1.95
53
-
optimum temperature for 3-phospho-D-glycerate oxidation
Sulfurisphaera tokodaii
1.1.1.95
80
-
optimum for 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
Temperature Stability [°C]
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.95
50
80
enzyme is highly thermostable, retaining more than 90% of its activity after incubation for 1 h at 80°C
Sulfurisphaera tokodaii
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.95
7.5
-
3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
1.1.1.95
10
-
3-phospho-D-glycerate oxidation
Sulfurisphaera tokodaii
pH Stability
EC Number
pH Stability
pH Stability Maximum
Commentary
Organism
1.1.1.95
3.5
11.5
enzyme is stable over a wide range of pHs. No decrease in activity after 20 min incubation at 50°C
Sulfurisphaera tokodaii
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.95
NAD+
-
Sulfurisphaera tokodaii
1.1.1.95
NADP+
NADP utilization is not observed in the forward reaction even in the presence of high concentrations of 10 mM NADP and 10 mM 3-phospho-D-glycerate
Sulfurisphaera tokodaii
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
1.1.1.95
2
-
K2HPO4
value of phosphate against 3-phosphohydroxypyruvate
Sulfurisphaera tokodaii
1.1.1.95
10
-
K2HPO4
value of phosphate against NADPH
Sulfurisphaera tokodaii
Activating Compound (protein specific)
EC Number
Activating Compound
Commentary
Organism
Structure
1.1.1.95
(NH4)2SO4
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
1.1.1.95
K2HPO4
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.95
expressed in Escherichia coli
Sulfurisphaera tokodaii
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.95
NAD+
-
Sulfurisphaera tokodaii
1.1.1.95
NADP+
NADP utilization is not observed in the forward reaction even in the presence of high concentrations of 10 mM NADP and 10 mM 3-phospho-D-glycerate
Sulfurisphaera tokodaii
General Stability (protein specific)
EC Number
General Stability
Organism
1.1.1.95
enzyme is highly thermostable
Sulfurisphaera tokodaii
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.95
(NH4)2SO4
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
1.1.1.95
3-phosphohydroxypyruvate
product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: 3-phospho-D-glycerate, inhibition pattern: competitive; product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: NAD, inhibition pattern: non-competitive
Sulfurisphaera tokodaii
1.1.1.95
ADP
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 86%
Sulfurisphaera tokodaii
1.1.1.95
AMP
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 75%
Sulfurisphaera tokodaii
1.1.1.95
ATP
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 85%
Sulfurisphaera tokodaii
1.1.1.95
K2HPO4
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction. It appears that the phosphate ion PO43- exerts its inhibitory effect by binding to the free enzyme and NADPH-enzyme complex
Sulfurisphaera tokodaii
1.1.1.95
additional information
unlike the Escherichia coli PGDH no inhibition by L-serine
Sulfurisphaera tokodaii
1.1.1.95
NADH
product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: 3-phospho-D-glycerate, inhibition pattern: non-competitive; product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: NAD, inhibition pattern: competitive
Sulfurisphaera tokodaii
1.1.1.95
ZnCl2
inhibitory effect on 3-phosphohydroxypyruvate reduction, remaining activity: 29%
Sulfurisphaera tokodaii
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
1.1.1.95
2
-
K2HPO4
value of phosphate against 3-phosphohydroxypyruvate
Sulfurisphaera tokodaii
1.1.1.95
10
-
K2HPO4
value of phosphate against NADPH
Sulfurisphaera tokodaii
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.95
0.0013
-
NADH
value for 3-phosphohydroxypyruvate reduction using NADH as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.0096
-
3-phosphohydroxypyruvate
value for 3-phosphohydroxypyruvate reduction using NADH as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.02
-
NADPH
value for 3-phosphohydroxypyruvate reduction using NADPH as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.033
-
3-phospho-D-glycerate
value for 3-phospho-D-glycerate oxidation using NAD+ as a cofactor
Sulfurisphaera tokodaii
1.1.1.95
0.04
-
NAD+
value for 3-phospho-D-glycerate oxidation
Sulfurisphaera tokodaii
1.1.1.95
0.12
-
3-phosphohydroxypyruvate
value for 3-phosphohydroxypyruvate reduction using NADPH as a cofactor
Sulfurisphaera tokodaii
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.95
35000
-
SDS-PAGE
Sulfurisphaera tokodaii
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.95
using a butyl Sepharose 4 Fast Flow column and a Superdex 200 gel filtration column. During purification an unexpected decline in enzyme activity is observed if the enzyme is stored in plastic tubes, but not in glass ones
Sulfurisphaera tokodaii
Specific Activity [micromol/min/mg] (protein specific)
EC Number
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
1.1.1.95
additional information
-
during purification an unexpected decline in enzyme activity is observed if the enzyme is stored in plastic tubes, but not in glass ones
Sulfurisphaera tokodaii
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.95
2-phospho-D-glycerate + NAD+
activity relative to 3-phospho-D-glycerate: 47%
684698
Sulfurisphaera tokodaii
2-phosphohydroxypyruvate + NADH + H+
-
-
-
?
1.1.1.95
3-phospho-D-glycerate + NAD+
highest activity
684698
Sulfurisphaera tokodaii
3-phosphohydroxypyruvate + NADH + H+
-
-
-
r
1.1.1.95
3-phospho-D-glycerate + NADP+
-
684698
Sulfurisphaera tokodaii
3-phosphohydroxypyruvate + NADPH + H+
-
-
-
r
1.1.1.95
DL-glyceraldehyde 3-phosphate + NAD+
activity relative to 3-phospho-D-glycerate: 9%
684698
Sulfurisphaera tokodaii
?
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.95
homodimer
gel filtration
Sulfurisphaera tokodaii
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.95
50
-
assay at
Sulfurisphaera tokodaii
1.1.1.95
53
-
optimum temperature for 3-phospho-D-glycerate oxidation
Sulfurisphaera tokodaii
1.1.1.95
80
-
optimum for 3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
Temperature Stability [°C] (protein specific)
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.95
50
80
enzyme is highly thermostable, retaining more than 90% of its activity after incubation for 1 h at 80°C
Sulfurisphaera tokodaii
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.95
7.5
-
3-phosphohydroxypyruvate reduction
Sulfurisphaera tokodaii
1.1.1.95
10
-
3-phospho-D-glycerate oxidation
Sulfurisphaera tokodaii
pH Stability (protein specific)
EC Number
pH Stability
pH Stability Maximum
Commentary
Organism
1.1.1.95
3.5
11.5
enzyme is stable over a wide range of pHs. No decrease in activity after 20 min incubation at 50°C
Sulfurisphaera tokodaii