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Literature summary for 2.2.1.7 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
Search for more literature for 2.2.1.7

Cloned(Commentary)

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

Protein Variants

Protein Variants Comment Organism
D430A the mutant shows 9 and 50% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
H340A the mutant shows 7 and 2% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
H434A the mutant shows 30 and more than 20% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
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
N181A the mutant shows 9 and 70% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
N183A inactive Deinococcus radiodurans
R423A inactive Deinococcus radiodurans
R423K the mutant shows 7 and 250% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
Y395A the mutant shows 4 and 80% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans
Y395F the mutant shows 9 and 60% of wild type activity for D-glyceraldehyde 3-phosphate and pyruvate, respectively Deinococcus radiodurans

Inhibitors

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

KM Value [mM]

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

Metals/Ions

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

Natural Substrates/ Products (Substrates)

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

Organism

Organism UniProt Comment Textmining
Deinococcus radiodurans Q9RUB5
-
-
Deinococcus radiodurans DSM 20539 Q9RUB5
-
-

Purification (Commentary)

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

Substrates and Products (Substrate)

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

Subunits

Subunits Comment Organism
homodimer
-
 Deinococcus radiodurans

Synonyms

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

Turnover Number [1/s]

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

Cofactor

Cofactor Comment Organism Structure
thiamine diphosphate dependent on Deinococcus radiodurans

Ki Value [mM]

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

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