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Literature summary extracted from

  • Handa, S.; Dempsey, D.R.; Ramamoorthy, D.; Cook, N.; Guida, W.C.; Spradling, T.J.; White, J.K.; Woodcock, H.L.; Merkler, D.J.
    Mechanistic studies of 1-deoxy-D-xylulose-5-phosphate synthase from Deinococcus radiodurans (2018), Biochem. Mol. Biol. J., 4, 2 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.2.1.7 expressed in Escherichia coli BL-21 B (DE3) cells Deinococcus radiodurans

Protein Variants

EC Number Protein Variants Comment Organism
2.2.1.7 D430A the mutant shows 9 and 50% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
2.2.1.7 H340A the mutant shows 7 and 2% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
2.2.1.7 H434A the mutant shows 30 and more than 20% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
2.2.1.7 H82A the KM values for the mutant for both D-glyceraldehyde 3-phosphate and pyruvate are similar to the wild type enzyme. The mutant shows 9 and 7% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
2.2.1.7 N181A the mutant shows 9 and 70% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
2.2.1.7 N183A inactive Deinococcus radiodurans
2.2.1.7 R423A inactive Deinococcus radiodurans
2.2.1.7 R423K the mutant shows 7 and 250% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
2.2.1.7 Y395A the mutant shows 4 and 80% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
2.2.1.7 Y395F the mutant shows 9 and 60% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.2.1.7 1-deoxy-D-xylulose 5-phosphate competitive inhibition with respect to pyruvate, non-competitive inhibition with respect to D-glyceraldehyde 3-phosphate Deinococcus radiodurans
2.2.1.7 beta-fluoropyruvate competitive inhibition with respect to pyruvate, non-competitive inhibition with respect to D-glyceraldehyde 3-phosphate Deinococcus radiodurans

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.2.1.7 0.03
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H82A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.03
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme N181A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.05
-
 pyruvate apparent value, mutant enzyme H434K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.05
-
 D-glyceraldehyde 3-phosphate apparent value, wild type enzyme, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.06
-
 pyruvate apparent value, mutant enzyme R423K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.08
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H304A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.12
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme D430A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.16
-
 pyruvate apparent value, mutant enzyme Y395A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.17
-
 pyruvate apparent value, mutant enzyme N181A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.19
-
 pyruvate apparent value, mutant enzyme Y395F, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.23
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H434A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.23
-
 pyruvate apparent value, mutant enzyme H82A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.28
-
 pyruvate apparent value, wild type enzyme, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.52
-
 pyruvate apparent value, mutant enzyme D430A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.59
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme Y395A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.6
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme R423K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.67
-
 D-glyceraldehyde 3-phosphate apparent value, wild type enzyme, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 1.7
-
 pyruvate apparent value, mutant enzyme H304A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 7.7
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme Y395F, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 12
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme R423A, at pH 8.0 and 37°C Deinococcus radiodurans

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.2.1.7 Mg2+ dependent on Deinococcus radiodurans

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.2.1.7 pyruvate + D-glyceraldehyde 3-phosphate Deinococcus radiodurans
-
 1-deoxy-D-xylulose 5-phosphate + CO2
-
 ?
2.2.1.7 pyruvate + D-glyceraldehyde 3-phosphate Deinococcus radiodurans DSM 20539
-
 1-deoxy-D-xylulose 5-phosphate + CO2
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.2.1.7 Deinococcus radiodurans Q9RUB5
-
-
2.2.1.7 Deinococcus radiodurans DSM 20539 Q9RUB5
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.2.1.7 Ni-NTA resin column chromatography Deinococcus radiodurans

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.2.1.7 pyruvate + D-glyceraldehyde 3-phosphate
-
 Deinococcus radiodurans 1-deoxy-D-xylulose 5-phosphate + CO2
-
 ?
2.2.1.7 pyruvate + D-glyceraldehyde 3-phosphate
-
 Deinococcus radiodurans DSM 20539 1-deoxy-D-xylulose 5-phosphate + CO2
-
 ?

Subunits

EC Number Subunits Comment Organism
2.2.1.7 homodimer
-
 Deinococcus radiodurans

Synonyms

EC Number Synonyms Comment Organism
2.2.1.7 1-deoxy-D-xylulose-5-phosphate synthase
-
 Deinococcus radiodurans
2.2.1.7 DXPS
-
 Deinococcus radiodurans

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.2.1.7 0.37
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H82A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.38
-
 pyruvate apparent value, mutant enzyme H82A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.43
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme N181A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.9
-
 pyruvate apparent value, mutant enzyme H304A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.9
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H304A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 1.7
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme R423A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 2.9
-
 pyruvate apparent value, mutant enzyme Y395F, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 3.3
-
 pyruvate apparent value, mutant enzyme N181A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 3.6
-
 pyruvate apparent value, mutant enzyme Y395A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 3.9
-
 pyruvate apparent value, mutant enzyme R423K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 3.9
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme Y395A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 5.9
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme Y395F, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 6.4
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme R423K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 7.2
-
 pyruvate apparent value, mutant enzyme D430A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 7.4
-
 pyruvate apparent value, wild type enzyme, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 7.7
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme D430A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 7.9
-
 D-glyceraldehyde 3-phosphate apparent value, wild type enzyme, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 9.6
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H434A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 9.9
-
 pyruvate apparent value, mutant enzyme H434K, at pH 8.0 and 37°C Deinococcus radiodurans

Cofactor

EC Number Cofactor Comment Organism Structure
2.2.1.7 thiamine diphosphate dependent on Deinococcus radiodurans

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
2.2.1.7 0.0033
-
 beta-fluoropyruvate inhibition with respect to pyruvate, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.057
-
 beta-fluoropyruvate inhibition with respect to D-glyceraldehyde 3-phosphate, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.13
-
 1-deoxy-D-xylulose 5-phosphate inhibition with respect to pyruvate, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.83
-
 1-deoxy-D-xylulose 5-phosphate inhibition with respect to D-glyceraldehyde 3-phosphate, at pH 8.0 and 37°C Deinococcus radiodurans

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2.2.1.7 0.14
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme R423A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.58
-
 pyruvate apparent value, mutant enzyme H304A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 0.59
-
 pyruvate apparent value, mutant enzyme H434K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 1.7
-
 pyruvate apparent value, mutant enzyme H82A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 5.8
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme Y395A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 10
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme Y395F, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 11
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H304A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 11
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme R423K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 13
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H82A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 14
-
 pyruvate apparent value, mutant enzyme D430A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 14
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme N181A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 16
-
 pyruvate apparent value, mutant enzyme Y395F, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 19
-
 pyruvate apparent value, mutant enzyme N181A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 22
-
 pyruvate apparent value, mutant enzyme Y395A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 26
-
 pyruvate apparent value, wild type enzyme, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 42
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme H434A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 65
-
 pyruvate apparent value, mutant enzyme R423K, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 66
-
 D-glyceraldehyde 3-phosphate apparent value, mutant enzyme D430A, at pH 8.0 and 37°C Deinococcus radiodurans
2.2.1.7 150
-
 D-glyceraldehyde 3-phosphate apparent value, wild type enzyme, at pH 8.0 and 37°C Deinococcus radiodurans