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Literature summary for 1.1.1.25 extracted from

  • Tahara, K.; Nishiguchi, M.; Funke, E.; Miyazawa, S.I.; Miyama, T.; Milkowski, C.
    Dehydroquinate dehydratase/shikimate dehydrogenases involved in gallate biosynthesis of the aluminum-tolerant tree species Eucalyptus camaldulensis (2020), Planta, 253, 3 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 1.1.1.25

Cloned(Commentary)

Cloned (Comment) Organism
expression in Escherichia coli as recombinant N-terminal GST-tagged protein Eucalyptus camaldulensis
gene EcDQD/SDH1, DNA and amino acid sequence determination and analysis, phylogenetic analysis, recombinant expression of GST-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIL, quantitative real-time RT-PCR enzyme expression analysis Eucalyptus camaldulensis
gene EcDQD/SDH2, DNA and amino acid sequence determination and analysis, phylogenetic analysis, recombinant expression of GST-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIL, quantitative real-time RT-PCR enzyme expression analysis Eucalyptus camaldulensis
gene EcDQD/SDH3, DNA and amino acid sequence determination and analysis, phylogenetic analysis, recombinant expression of GST-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIL, quantitative real-time RT-PCR enzyme expression analysis Eucalyptus camaldulensis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.00438
-
 NADPH pH 8.5, temperature not specified in the publication Eucalyptus camaldulensis
0.00438
-
 NADPH pH 8.5, 30°C, EcDQD/SDH2, shikimate formation Eucalyptus camaldulensis
0.0231
-
 NADPH pH 6.5, 30°C, EcDQD/SDH3, shikimate formation Eucalyptus camaldulensis
0.0326
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
0.0326
-
 shikimate pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
0.0415
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
0.0415
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH3, shikimate oxidation Eucalyptus camaldulensis
0.0495
-
 NADPH pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
0.0495
-
 NADPH pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
0.0565
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
0.0565
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
0.0652
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
0.0652
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH2, shikimate oxidation Eucalyptus camaldulensis
0.322
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH2, DQD activity Eucalyptus camaldulensis
0.381
-
 3-dehydroshikimate pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
0.381
-
 3-dehydroshikimate pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
0.449
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH1, DQD activity Eucalyptus camaldulensis
0.878
-
 3-dehydroshikimate pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
0.878
-
 3-dehydroshikimate pH 6.5, 30°C, EcDQD/SDH3, shikimate formation Eucalyptus camaldulensis
0.882
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH3, DQD activity Eucalyptus camaldulensis
2.05
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
2.05
-
 shikimate pH 9.0, 30°C, EcDQD/SDH2, shikimate oxidation Eucalyptus camaldulensis
3.64
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
3.64
-
 shikimate pH 9.0, 30°C, EcDQD/SDH3, shikimate oxidation Eucalyptus camaldulensis
8.83
-
 3-dehydroshikimate pH 8.5, temperature not specified in the publication Eucalyptus camaldulensis
8.83
-
 3-dehydroshikimate pH 8.5, 30°C, EcDQD/SDH2, shikimate formation Eucalyptus camaldulensis
9.44
-
 3-dehydroshikimate pH 10.5, 30°C, EcDQD/SDH2, gallate formation Eucalyptus camaldulensis
23.1
-
 NADPH pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
30.6
-
 3-dehydroshikimate pH 10.5, 30°C, EcDQD/SDH2, gallate formation Eucalyptus camaldulensis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3-dehydroshikimate + NADP+ Eucalyptus camaldulensis
-
 gallate + NADPH + H+
-
 r
shikimate + NADP+ Eucalyptus camaldulensis
-
 3-dehydroshikimate + NADPH + H+
-
 r

Organism

Organism UniProt Comment Textmining
Eucalyptus camaldulensis A0A5H2WVH6
-
-
Eucalyptus camaldulensis A0A5H2WZU5
-
-
Eucalyptus camaldulensis A0A5H2X4C4
-
-

Purification (Commentary)

Purification (Comment) Organism
-
 Eucalyptus camaldulensis
recombinant GST-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIL by glutathione affinity chromatography and tag cleavage through thrombin Eucalyptus camaldulensis

Source Tissue

Source Tissue Comment Organism Textmining
leaf
-
 Eucalyptus camaldulensis
-
leaf highest expression level Eucalyptus camaldulensis
-
additional information comparison of EcDQD/SDH, UGT84A25a/b, and UGT84A26a/b expression patterns in Eucalyptus camaldulensis, relative EcDQD/SDH mRNA levels in the leaves, stems, and roots are plotted against the relative UGT84A25a/b and UGT84A26a/b mRNA levels in the same samples, and determination of concentrations of the metabolites in the different tissues, overview Eucalyptus camaldulensis
-
root
-
 Eucalyptus camaldulensis
-
root lowest expression level Eucalyptus camaldulensis
-
stem highest expression level Eucalyptus camaldulensis
-
stem lowest expression level Eucalyptus camaldulensis
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3-dehydroshikimate + NADP+
-
 Eucalyptus camaldulensis gallate + NADPH + H+
-
 r
3-dehydroshikimate + NADPH + H+
-
 Eucalyptus camaldulensis shikimate + NADP+
-
 r
additional information product analysis by GC-MS. No or poor quinate dehydrogenase activity Eucalyptus camaldulensis ?
-
-
shikimate + NADP+
-
 Eucalyptus camaldulensis 3-dehydroshikimate + NADPH + H+
-
 r

Synonyms

Synonyms Comment Organism
dehydroquinate dehydratase/shikimate dehydrogenase
-
 Eucalyptus camaldulensis
EcDQD
-
 Eucalyptus camaldulensis
EcDQD/SDH
-
 Eucalyptus camaldulensis
EcDQD/SDH1
-
 Eucalyptus camaldulensis
EcDQD/SDH2
-
 Eucalyptus camaldulensis
EcDQD/SDH3
-
 Eucalyptus camaldulensis
More cf. EC 4.2.1.10 Eucalyptus camaldulensis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
 assay at Eucalyptus camaldulensis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.14
-
 3-dehydroshikimate pH 10.5, 30°C, EcDQD/SDH2, gallate formation Eucalyptus camaldulensis
2.87
-
 3-dehydroshikimate pH 10.5, 30°C, EcDQD/SDH2, gallate formation Eucalyptus camaldulensis
3.67
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH1, DQD activity Eucalyptus camaldulensis
27.6
-
 NADPH pH 8.5, temperature not specified in the publication Eucalyptus camaldulensis
27.6
-
 NADPH pH 8.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
30.9
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH1, DQD activity Eucalyptus camaldulensis
47
-
 3-dehydroshikimate pH 8.5, temperature not specified in the publication Eucalyptus camaldulensis
47
-
 3-dehydroshikimate pH 8.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
57.6
-
 3-dehydroshikimate pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
57.6
-
 3-dehydroshikimate pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
60.4
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH1, DQD activity Eucalyptus camaldulensis
70.2
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
70.2
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
74.1
-
 NADPH pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
74.1
-
 NADPH pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
80.7
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
80.7
-
 shikimate pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
135
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
135
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
146
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
146
-
 shikimate pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
307
-
 3-dehydroshikimate pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
307
-
 3-dehydroshikimate pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
389
-
 NADPH pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
389
-
 NADPH pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
755
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
755
-
 shikimate pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
792
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
792
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
6.5
-
 shikimate formation activity Eucalyptus camaldulensis
7
-
 DQD activity Eucalyptus camaldulensis
7.5
-
 quinate formation activity Eucalyptus camaldulensis
8.5
-
 shikimate formation activity Eucalyptus camaldulensis
9
-
 shikimate and quinate oxidation Eucalyptus camaldulensis
10.5
-
 gallate formation activity Eucalyptus camaldulensis

Cofactor

Cofactor Comment Organism Structure
NADP+
-
 Eucalyptus camaldulensis
NADP+ the enzyme shows a clear preference for NADPH/NADP+ over NADH/ NAD+ Eucalyptus camaldulensis
NADPH
-
 Eucalyptus camaldulensis
NADPH the enzyme shows a clear preference for NADPH/NADP+ over NADH/ NAD+ Eucalyptus camaldulensis

General Information

General Information Comment Organism
evolution plant SDH enzymes are fused to dehydroquinate dehydratases (DQDs, EC 4.2.1.10) to form bifunctional DQD/SDH enzymes. The DQD activity is observed for EcDQD/SDH1, 2, and 3, but not for EcDQD/SDH4a. Among the active enzymes, EcDQD/SDH1 exhibits the highest DQD activity, followed by EcDQD/SDH2 (about 50% of the EcDQD/SDH1 activity) and EcDQD/SDH3 (about 5% of the EcDQD/SDH1 activity). For shikimate formation from 3-DHS as well as shikimate oxidation to 3-DHS, measurable catalytic activities are detected for EcDQD/SDH1-3, but the activities of EcDQD/SDH2 and 3 are less than 20% of those of EcDQD/SDH1. Regarding the cofactor, EcDQD/SDH1-3 have a clear preference for NADPH/NADP+ over NADH/ NAD+. In contrast, EcDQD/SDH4a and b lack shikimate formation activity. For the reverse reaction, the conversion of shikimate to 3-DHS, EcDQD/SDH4a and b display low enzymatic activity with a preference for NAD+ as the cofactor. Both EcDQD/SDH2 and 3 exhibit relatively high gallate formation activity, in contrast to the low activity of EcDQD/SDH1. The preferred cofactor in this reaction is NADP+ Eucalyptus camaldulensis
metabolism shikimate, quinate, and gallate biosynthesis catalyzed by DQD/SDH family enzymes, overview. Plant DQD/SDHs are proposed to link the shikimate pathway to gallate and quinate metabolism Eucalyptus camaldulensis
metabolism shikimate, quinate, and gallate biosynthesis catalyzed by DQD/SDH family enzymes, overview. Plant DQD/SDHs are proposed to link the shikimate pathway to gallate and quinate metabolism. Isozymes EcDQD/SDH2 and 3 from Eucalyptus camaldulensis catalyze the NADP+-dependent oxidation of 3-dehydroshikimate to produce gallate. In Eucalyptus camaldulensis, EcDQD/SDH2 and 3 are co-expressed with UGT84A25a/b and UGT84A26a/b involved in hydrolyzable tannin biosynthesis, catalyze the synthesis of beta-glucogallin Eucalyptus camaldulensis
metabolism shikimate, quinate, and gallate biosynthesis catalyzed by DQD/SDH family enzymes, overview. Plant DQD/SDHs are proposed to link the shikimate pathway to gallate and quinate metabolism. Isozymes EcDQD/SDH2 and 3 from Eucalyptus camaldulensis catalyze the NADP+-dependent oxidation of 3-dehydroshikimate to produce gallate. In Eucalyptus camaldulensis, EcDQD/SDH2 and 3 are co-expressed with UGT84A25a/b and UGT84A26a/b involved in hydrolyzable tannin biosynthesis, they catalyze the synthesis of beta-glucogallin Eucalyptus camaldulensis
additional information EcDQD/SDH1 enzyme structure homology modeling using the structure of Arabidopsis thaliana AtDQD/SDH (Uniprot ID Q9SQT8) as template, docking of 3-dehydroshikimate into the active site of the models as well as the crystal structure of PDB ID 2O7S, molecular dynamics simulation of protein-ligand interaction Eucalyptus camaldulensis
additional information EcDQD/SDH2 enzyme structure homology modeling using the structure of Arabidopsis thaliana AtDQD/SDH (Uniprot ID Q9SQT8) as template, docking of 3-dehydroshikimate into the active site of the models as well as the crystal structure of PDB ID 2O7S, molecular dynamics simulation of protein-ligand interaction Eucalyptus camaldulensis
additional information EcDQD/SDH3 enzyme structure homology modeling using the structure of Arabidopsis thaliana AtDQD/SDH (Uniprot ID Q9SQT8) as template, docking of 3-dehydroshikimate into the active site of the models as well as the crystal structure of PDB ID 2O7S, molecular dynamics simulation of protein-ligand interaction Eucalyptus camaldulensis
physiological function the tree species Eucalyptus camaldulensis shows exceptionally high tolerance against aluminum, a widespread toxic metal in acidic soils. In the roots of Eucalyptus camaldulensis, aluminum is detoxified via the complexation with oenothein B, a hydrolyzable tannin. The biosynthesis of oenothein B involves dehydroquinate dehydratase/shikimate dehydrogenases (EcDQD/SDHs) which catalyzes the formation of gallate, the phenolic constituent of hydrolyzable tannins Eucalyptus camaldulensis
physiological function the tree species Eucalyptus camaldulensis shows exceptionally high tolerance against aluminum, a widespread toxic metal in acidic soils. In the roots of Eucalyptus camaldulensis, aluminum is detoxified via the complexation with oenothein B, a hydrolyzable tannin. The biosynthesis of oenothein B involves dehydroquinate dehydratase/shikimate dehydrogenases (EcDQD/SDHs) which catalyzes the formation of gallate, the phenolic constituent of hydrolyzable tannins. Two enzymes, EcDQD/SDH2 and 3, in Eucalyptus camaldulensis catalyze the NADP+-dependent oxidation of 3-dehydroshikimate to produce gallate. EcDQD/SDH2 and 3 maintain DQD and SDH activities, resulting in a 3-dehydroshikimate supply for gallate formation Eucalyptus camaldulensis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.07
-
 3-dehydroshikimate pH 10.5, 30°C, EcDQD/SDH2, gallate formation Eucalyptus camaldulensis
0.304
-
 3-dehydroshikimate pH 10.5, 30°C, EcDQD/SDH2, gallate formation Eucalyptus camaldulensis
4.16
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH3, DQD activity Eucalyptus camaldulensis
5.32
-
 3-dehydroshikimate pH 8.5, temperature not specified in the publication Eucalyptus camaldulensis
5.32
-
 3-dehydroshikimate pH 8.5, 30°C, EcDQD/SDH2, shikimate formation Eucalyptus camaldulensis
22.17
-
 shikimate pH 9.0, 30°C, EcDQD/SDH3, shikimate oxidation Eucalyptus camaldulensis
22.2
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
65.6
-
 3-dehydroshikimate pH 6.5, 30°C, EcDQD/SDH3, shikimate formation Eucalyptus camaldulensis
65.6
-
 3-dehydroshikimate pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
71.2
-
 shikimate pH 9.0, 30°C, EcDQD/SDH2, shikimate oxidation Eucalyptus camaldulensis
71.3
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
96
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH2, DQD activity Eucalyptus camaldulensis
134.5
-
 3-dehydroshikimate pH 7.0, 30°C, EcDQD/SDH1, DQD activity Eucalyptus camaldulensis
805
-
 3-dehydroshikimate pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
805.8
-
 3-dehydroshikimate pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
1690
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
1691.6
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH3, shikimate oxidation Eucalyptus camaldulensis
2070
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
2070.6
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH2, shikimate oxidation Eucalyptus camaldulensis
3207.8
-
 NADPH pH 6.5, 30°C, EcDQD/SDH3, shikimate formation Eucalyptus camaldulensis
3210
-
 NADPH pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
6300
-
 NADPH pH 8.5, temperature not specified in the publication Eucalyptus camaldulensis
6301.4
-
 NADPH pH 8.5, 30°C, EcDQD/SDH2, shikimate formation Eucalyptus camaldulensis
7858.6
-
 NADPH pH 6.5, 30°C, EcDQD/SDH1, shikimate formation Eucalyptus camaldulensis
7860
-
 NADPH pH 6.5, temperature not specified in the publication Eucalyptus camaldulensis
14000
-
 NADP+ pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis
14017.7
-
 NADP+ pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
23159.5
-
 shikimate pH 9.0, 30°C, EcDQD/SDH1, shikimate oxidation Eucalyptus camaldulensis
23200
-
 shikimate pH 9.0, temperature not specified in the publication Eucalyptus camaldulensis