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Literature summary extracted from
- Molecular characterization of quinate and shikimate metabolism in Populus trichocarpa (2014), J. Biol. Chem., 289, 23846-23858.
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 1.1.1.25 | recombinant His6-tagged DQD/SDH isozyme 1 overexpression in Escherichia coli strain M15 | Populus trichocarpa |
| 1.1.1.25 | recombinant His6-tagged DQD/SDH isozyme 5 overexpression in Escherichia coli strain M15 | Populus trichocarpa |
| 1.1.1.282 | recombinant expression of His6-tagged isozymes in Escherichia coli strain M15 | Populus trichocarpa |
KM Value [mM]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 1.1.1.25 | additional information | - |
additional information | Michaelis-Menten kinetics | Populus trichocarpa | |
| 1.1.1.25 | 0.223 | - |
shikimate | with NADP+, pH 8.5, 22°C, recombinant His-tagged Poptr1 | Populus trichocarpa |  |
| 1.1.1.25 | 0.321 | - |
shikimate | with NADP+, pH 8.5, 22°C, recombinant His-tagged Poptr1 | Populus trichocarpa | |
| 1.1.1.25 | 0.346 | - |
shikimate | with NAD+, pH 8.5, 22°C, recombinant His-tagged Poptr1 | Populus trichocarpa | |
| 1.1.1.25 | 0.427 | - |
shikimate | with NAD+, pH 8.5, 22°C, recombinant His-tagged Poptr1 | Populus trichocarpa | |
| 1.1.1.282 | additional information | - |
additional information | Michaelis-Menten kinetics | Populus trichocarpa | |
| 1.1.1.282 | 0.321 | - |
L-quinate | with NAD+, isozyme Poptr3, pH 8.5, 22°C | Populus trichocarpa | |
| 1.1.1.282 | 0.334 | - |
L-quinate | with NAD+, isozyme Poptr2, pH 8.5, 22°C | Populus trichocarpa | |
| 1.1.1.282 | 0.392 | - |
shikimate | with NAD+, isozyme Poptr3, pH 8.5, 22°C | Populus trichocarpa | |
| 1.1.1.282 | 0.833 | - |
shikimate | with NAD+, isozyme Poptr2, pH 8.5, 22°C | Populus trichocarpa | |
Localization
| EC Number | Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|---|
| 1.1.1.25 | chloroplast | - |
Populus trichocarpa | 9507 | - |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.1.1.25 | 3-dehydroquinate | Populus trichocarpa | - |
3-dehydroshikimate + H2O | - |
r | |
| 1.1.1.25 | 3-dehydroquinate | Populus trichocarpa Nisqually-1 | - |
3-dehydroshikimate + H2O | - |
r | |
| 1.1.1.25 | 3-dehydroshikimate + NADPH | Populus trichocarpa | - |
shikimate + NADP+ | - |
r | |
| 1.1.1.25 | additional information | Populus trichocarpa | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | ? | - |
? | |
| 1.1.1.25 | additional information | Populus trichocarpa | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD3/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | ? | - |
? | |
| 1.1.1.25 | additional information | Populus trichocarpa Nisqually-1 | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | ? | - |
? | |
| 1.1.1.25 | additional information | Populus trichocarpa Nisqually-1 | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD3/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | ? | - |
? | |
| 1.1.1.282 | L-quinate + NAD+ | Populus trichocarpa | - |
3-dehydroquinate + NADH + H+ | - |
? | |
| 1.1.1.282 | additional information | Populus trichocarpa | the enzyme preferentially uses quinate as a substrate in vitro like a quinate dehydrogenase, EC 1.1.1.24, with only residual shikimate dehydrogenase, SDH, activity, cf. EC 1.1.1.25 | ? | - |
? | |
| 1.1.1.282 | shikimate + NAD+ | Populus trichocarpa | - |
3-dehydroshikimate + NADH + H+ | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 1.1.1.25 | Populus trichocarpa | - |
trees grown in a field at the University of Victoria, Victoria, British Columbia, Canada | - |
| 1.1.1.25 | Populus trichocarpa Nisqually-1 | - |
trees grown in a field at the University of Victoria, Victoria, British Columbia, Canada | - |
| 1.1.1.282 | Populus trichocarpa | - |
trees grown in a field at the University of Victoria | - |
| 1.1.1.282 | Populus trichocarpa Nisqually-1 | - |
trees grown in a field at the University of Victoria | - |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 1.1.1.25 | recombinant His6-tagged DQD/SDH isozyme 5 from Escherichia coli strain M15 by nickel affinity chromatography | Populus trichocarpa |
| 1.1.1.282 | recombinant His6-tagged isozymes from Escherichia coli strain M15 by nickel affinity chromatography | Populus trichocarpa |
Source Tissue
| EC Number | Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|---|
| 1.1.1.25 | bark | - |
Populus trichocarpa | - |
| 1.1.1.25 | leaf | - |
Populus trichocarpa | - |
| 1.1.1.25 | additional information | poplar DQD/SDHs have distinct expression profiles, organ-specific expression of poplar DQD/SDHs, overview | Populus trichocarpa | - |
| 1.1.1.25 | phloem | - |
Populus trichocarpa | - |
| 1.1.1.25 | xylem | - |
Populus trichocarpa | - |
| 1.1.1.282 | bark | Poptr3 and Poptr4 | Populus trichocarpa | - |
| 1.1.1.282 | leaf | Poptr4 | Populus trichocarpa | - |
| 1.1.1.282 | additional information | Poptr4 shows a distinct expression pattern with predominant expression in leaves, seedlings, and stomata and some expression in bark and differentiating tissues. Isozyme expression profiles, overview | Populus trichocarpa | - |
| 1.1.1.282 | root | Poptr2 and Poptr3 are highly expressed in roots and root tips, respectively | Populus trichocarpa | - |
| 1.1.1.282 | seedling | Poptr4 | Populus trichocarpa | - |
| 1.1.1.282 | stem | Poptr3 is highly expressed in bark and some vascular tissues | Populus trichocarpa | - |
| 1.1.1.282 | stoma | Poptr4 | Populus trichocarpa | - |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.1.1.25 | 3-dehydroquinate | - |
Populus trichocarpa | 3-dehydroshikimate + H2O | - |
r | |
| 1.1.1.25 | 3-dehydroquinate | DQD reaction | Populus trichocarpa | 3-dehydroshikimate + H2O | - |
r | |
| 1.1.1.25 | 3-dehydroquinate | - |
Populus trichocarpa Nisqually-1 | 3-dehydroshikimate + H2O | - |
r | |
| 1.1.1.25 | 3-dehydroshikimate + NADH | SDH reaction, very low activity with NAD+ | Populus trichocarpa | shikimate + NAD+ | - |
r | |
| 1.1.1.25 | 3-dehydroshikimate + NADPH | - |
Populus trichocarpa | shikimate + NADP+ | - |
r | |
| 1.1.1.25 | 3-dehydroshikimate + NADPH | SDH reaction | Populus trichocarpa | shikimate + NADP+ | - |
r | |
| 1.1.1.25 | additional information | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | Populus trichocarpa | ? | - |
? | |
| 1.1.1.25 | additional information | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD3/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | Populus trichocarpa | ? | - |
? | |
| 1.1.1.25 | additional information | The bifunctional enzyme also catalyzes dehydration of 3-dehydroquinate to 3-dehydroshikimate. Under saturating conditions, Poptr5 displays strong activity with shikimate but no detectable activity with quinate even at elevated enzyme concentrations. The isozyme shows no quinate hydrolyase activity | Populus trichocarpa | ? | - |
? | |
| 1.1.1.25 | additional information | under saturating conditions, Poptr1 displays strong activity with shikimate but no detectable activity with quinate even at elevated enzyme concentrations. The isozyme shows no quinate hydrolyase activity | Populus trichocarpa | ? | - |
? | |
| 1.1.1.25 | additional information | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | Populus trichocarpa Nisqually-1 | ? | - |
? | |
| 1.1.1.25 | additional information | the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD3/SDH cf. EC 4.2.1.10 and EC 1.1.1.25) catalyzes the the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate | Populus trichocarpa Nisqually-1 | ? | - |
? | |
| 1.1.1.25 | additional information | The bifunctional enzyme also catalyzes dehydration of 3-dehydroquinate to 3-dehydroshikimate. Under saturating conditions, Poptr5 displays strong activity with shikimate but no detectable activity with quinate even at elevated enzyme concentrations. The isozyme shows no quinate hydrolyase activity | Populus trichocarpa Nisqually-1 | ? | - |
? | |
| 1.1.1.25 | additional information | under saturating conditions, Poptr1 displays strong activity with shikimate but no detectable activity with quinate even at elevated enzyme concentrations. The isozyme shows no quinate hydrolyase activity | Populus trichocarpa Nisqually-1 | ? | - |
? | |
| 1.1.1.25 | shikimate + NADP+ | SDH reaction | Populus trichocarpa | 3-dehydroshikimate + NADPH | - |
r | |
| 1.1.1.282 | L-quinate + NAD+ | - |
Populus trichocarpa | 3-dehydroquinate + NADH + H+ | - |
? | |
| 1.1.1.282 | additional information | the enzyme preferentially uses quinate as a substrate in vitro like a quinate dehydrogenase, EC 1.1.1.24, with only residual shikimate dehydrogenase, SDH, activity, cf. EC 1.1.1.25 | Populus trichocarpa | ? | - |
? | |
| 1.1.1.282 | shikimate + NAD+ | - |
Populus trichocarpa | 3-dehydroshikimate + NADH + H+ | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 1.1.1.25 | More | the DQD domain constitutes the N-terminal half of the protein and the SDH domain the C-terminal half. Three-dimensional protein structures homology modelling of the five putative poplar DQD/SDHs using Arabidopsis DQD/SDH enzyme structure, PDB ID c2o7qA, of the enzyme coupled with either 3-dehydroshikimate and tartrate or shikimate, as a template | Populus trichocarpa |
| 1.1.1.25 | More | three-dimensional protein structures homology modelling of the five putative poplar DQD/SDHs using Arabidopsis DQD/SDH enzyme structure, PDB ID c2o7qA, of the enzyme coupled with either 3-dehydroshikimate and tartrate or shikimate, as a template | Populus trichocarpa |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 1.1.1.25 | dehydroquinate dehydratase/shikimate dehydrogenase | - |
Populus trichocarpa |
| 1.1.1.25 | DQD/SDH | - |
Populus trichocarpa |
| 1.1.1.25 | Poptr1 | - |
Populus trichocarpa |
| 1.1.1.25 | Poptr5 | - |
Populus trichocarpa |
| 1.1.1.282 | Poptr2 | - |
Populus trichocarpa |
| 1.1.1.282 | Poptr3 | - |
Populus trichocarpa |
| 1.1.1.282 | Poptr4 | - |
Populus trichocarpa |
| 1.1.1.282 | SDH/QDH | - |
Populus trichocarpa |
| 1.1.1.282 | shikimate/quinate dehydrogenase | - |
Populus trichocarpa |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.25 | 22 | - |
assay at room temperature | Populus trichocarpa |
| 1.1.1.282 | 22 | - |
assay at room temperature | Populus trichocarpa |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.25 | 8.5 | - |
assay at | Populus trichocarpa |
| 1.1.1.282 | 8.5 | 9.5 | - |
Populus trichocarpa |
Cofactor
| EC Number | Cofactor | Comment | Organism | Structure |
|---|---|---|---|---|
| 1.1.1.25 | additional information | for Poptr5, no activity with shikimate is detectable in the presence of NAD+ even with elevated enzyme concentrations | Populus trichocarpa | |
| 1.1.1.25 | additional information | the highest enzyme activity is observed with NADP+, and activity drops by 96% when replacing NADP+ with NAD+ for Poptr1 | Populus trichocarpa | |
| 1.1.1.25 | NAD+ | very low activity | Populus trichocarpa | |
| 1.1.1.25 | NADH | very low activity | Populus trichocarpa | |
| 1.1.1.25 | NADP+ | - |
Populus trichocarpa | |
| 1.1.1.25 | NADPH | - |
Populus trichocarpa | |
| 1.1.1.282 | additional information | no activity with NADP+ | Populus trichocarpa | |
| 1.1.1.282 | NAD+ | - |
Populus trichocarpa | |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 1.1.1.25 | evolution | members of the same gene family encode enzymes with either shikimate or quinate dehydrogenase activity. The poplar genome encodes five DQD/SDH-like genes (Poptr1 to Poptr5), which have diverged into two distinct groups based on sequence analysis and protein structure prediction. In vitro biochemical assays prove that Poptr1 and -5 are true DQD/SDHs, whereas Poptr2 and -3 instead have QDH activity with only residual DQD/SDH activity, cf. EC 1.1.1.282 | Populus trichocarpa |
| 1.1.1.25 | metabolism | the shikimate pathway leads to the biosynthesis of aromatic amino acids essential for protein biosynthesis and the production of a wide array of plant secondary metabolites. 3-Dehydroquinate is the substrate for shikimate biosynthesis through the sequential actions of dehydroquinate dehydratase (DQD) and shikimate dehydrogenase (SDH) contained in a single protein in plants. Reactions comprising the shikimate/quinate cycle, overview | Populus trichocarpa |
| 1.1.1.25 | additional information | three-dimensional protein structures homology modelling of the five putative poplar DQD/SDHs using Arabidopsis DQD/SDH enzyme structure, PDB ID c2o7qA, of the enzyme coupled with either 3-dehydroshikimate and tartrate or shikimate, as a template | Populus trichocarpa |
| 1.1.1.25 | physiological function | the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate is catalyzed by the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH, EC 4.2.1.10 and E.C. 1.1.1.25). The DQD domain constitutes the N-terminal half of the protein and the SDH domain the C-terminal half. Poplar DQD/SDHs have distinct expression profiles suggesting separate roles in protein and lignin biosynthesis. Shikimate is essential for protein biosynthesis | Populus trichocarpa |
| 1.1.1.25 | physiological function | the conversion of 3-dehydroquinate to shikimate via 3-dehydroshikimate is catalyzed by the bifunctional enzyme dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH, EC 4.2.1.10 and EC 1.1.1.25). The DQD domain constitutes the N-terminal half of the protein and the SDH domain the C-terminal half. Poplar DQD/SDHs have distinct expression profiles suggesting separate roles in protein and lignin biosynthesis. Shikimate is essential for protein biosynthesis | Populus trichocarpa |
| 1.1.1.282 | evolution | members of the same gene family encode enzymes with either shikimate or quinate dehydrogenase activity. Plant SDHs are generally more similar to bacterial SDH/QDH YdiB (25-30% similarity) than to bacterial SDH AroE (21-28%) | Populus trichocarpa |
| 1.1.1.282 | metabolism | reactions comprising the shikimate/quinate cycle, overview | Populus trichocarpa |
| 1.1.1.282 | additional information | the enzymes have Gly residues instead of Ser residues in the active sites. The Ser-to-Gly conversion ompared to SDHs may generate extra space in the inferred Poptr isozymes active sites that can accommodate the hydroxyl group at the C1 position of quinate | Populus trichocarpa |
| 1.1.1.282 | physiological function | quinate and its derivatives are protective secondary metabolites, quinate is an astringent feeding deterrent that can be formed in a single step reaction from 3-dehydroquinate catalyzed by quinate dehydrogenase | Populus trichocarpa |
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