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Literature summary for 1.1.1.95 extracted from
- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana (2017), Sci. Rep., 7, 3533 .
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| L-alanine | 10 mM, activates | Arabidopsis thaliana |  |
| L-cysteine | 10 mM, activates | Arabidopsis thaliana | |
| L-homocysteine | 10 mM, activates | Arabidopsis thaliana | |
| L-homoserine | 10 mM, activates | Arabidopsis thaliana | |
| L-methionine | 10 mM, activates | Arabidopsis thaliana | |
| L-valine | 10 mM, activates | Arabidopsis thaliana | |
| additional information | AtPGDH2 activity is not affected by threonine, valine, glycine, tryptophan, O-acetyl-L-serine, or cysteine | Arabidopsis thaliana |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| expression in Escherichia coli | Arabidopsis thaliana |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| L-serine | 10 mM, inhibits AtPGDH3 at 55%; 10 mM, inhibits AtPGDH3 at 55% | Arabidopsis thaliana | |
| additional information | L-serine (10 mM) does not inhibit AtPGDH2 | Arabidopsis thaliana |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.05 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 0.088 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 0.123 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 0.5 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 0.77 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 1.03 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 3.7 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 3.9 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 7.6 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 10.7 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 11.2 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 14.1 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 60000 | - |
SDS-PAGE | Arabidopsis thaliana |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 3-phospho-D-glycerate + NAD+ | Arabidopsis thaliana | first committed enzyme of the phosphorylated pathway of l-serine biosynthesis, regulated by negative feedback from L-serine in bacteria and plants | 3-phosphooxypyruvate + NADH + H+ | - |
r | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Arabidopsis thaliana | O04130 | - |
- |
| Arabidopsis thaliana | O49485 | - |
- |
| Arabidopsis thaliana | Q9LT69 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
- |
Arabidopsis thaliana |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 2-oxoglutarate + NADH + H+ | - |
Arabidopsis thaliana | D-2-hydroxyglutarate + NAD+ | - |
? | |
| 3-phospho-D-glycerate + NAD+ | - |
Arabidopsis thaliana | 3-phosphooxypyruvate + NADH + H+ | - |
r | |
| 3-phospho-D-glycerate + NAD+ | first committed enzyme of the phosphorylated pathway of l-serine biosynthesis, regulated by negative feedback from L-serine in bacteria and plants | Arabidopsis thaliana | 3-phosphooxypyruvate + NADH + H+ | - |
r | |
| 3-phosphooxypyruvate + NADH + H+ | - |
Arabidopsis thaliana | 3-phospho-D-glycerate + NAD+ | - |
r | |
| oxaloacetate + NADH + H+ | - |
Arabidopsis thaliana | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| homooctamer | 8 * 60000, SDS-PAGE, AtPGDH2 forms an equilibrium of homooctamers and homotetramers | Arabidopsis thaliana |
| homotetramer | 4 * 60000, SDS-PAGE | Arabidopsis thaliana |
| homotetramer | 4 * 60000, SDS-PAGE, AtPGDH2 forms an equilibrium of homooctamers and homotetramers | Arabidopsis thaliana |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| 3-phosphoglycerate dehydrogenase | - |
Arabidopsis thaliana |
| At1g17745 | - |
Arabidopsis thaliana |
| At3g19480 | - |
Arabidopsis thaliana |
| At4g34200 | - |
Arabidopsis thaliana |
| PGDH | - |
Arabidopsis thaliana |
| PGDH1 | - |
Arabidopsis thaliana |
| PGDH2 | - |
Arabidopsis thaliana |
| PGDH3 | - |
Arabidopsis thaliana |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.00015 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.00018 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.0002 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.00051 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.00077 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.00135 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 15 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 15 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 16 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 16 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 17 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 17 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 6 | - |
optimal pH for reduction of 2-oxoglutarate and oxaloacetate | Arabidopsis thaliana |
| 9 | - |
substrate: 3-phospho-D-glycerate, AtPGDH1 | Arabidopsis thaliana |
| 9.5 | - |
substrate: 3-phospho-D-glycerate, AtPGDH3 | Arabidopsis thaliana |
| 10 | - |
substrate: 3-phospho-D-glycerate, AtPGDH2 | Arabidopsis thaliana |
Expression
| Organism | Comment | Expression |
|---|---|---|
| Arabidopsis thaliana | AtPGDH1 gene is coexpressed with genes of tryptophan biosynthesis. Activators of tryptophan biosynthesis MYB51 and MYB34 are involved in the expression of AtPGDH1 | up |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | tryptophan-derived metabolites such as indole acetic acid and indole glucosinolates are present at lower concentrations in AtPGDH1-silenced plants, demonstrating that serine used as a precursor for tryptophan biosynthesis is synthesized in the phosphorylated pathway, and that the involvement of AtPGDH1 is greatest among the three isoforms | Arabidopsis thaliana |
| metabolism | first committed enzyme of the phosphorylated pathway of L-serine biosynthesis, regulated by negative feedback from L-serine in bacteria and plants | Arabidopsis thaliana |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.000017 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.000019 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.000053 | - |
2-oxoglutarate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.000068 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.000131 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 0.000907 | - |
oxaloacetate | pH 6.0, 25°C | Arabidopsis thaliana | |
| 16 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 22 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 30 | - |
3-phospho-D-glycerate | pH 9.0, 25°C | Arabidopsis thaliana | |
| 130 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 190 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
| 300 | - |
NAD+ | pH 9.0, 25°C | Arabidopsis thaliana | |
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