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Literature summary extracted from

  • Gritsunov, A.; Peek, J.; Diaz Caballero, J.; Guttman, D.; Christendat, D.
    Structural and biochemical approaches uncover multiple evolutionary trajectories of plant quinate dehydrogenases (2018), Plant J., 95, 812-822 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.25 expression analysis, phylogenetic analysis Arabidopsis thaliana
1.1.1.282 gene expression analysis, phylogenetic analysis Nicotiana tabacum
1.1.1.282 gene expression analysis, phylogenetic analysis Brassica napus
1.1.1.282 gene expression analysis, phylogenetic analysis Brassica rapa
1.1.1.282 gene expression analysis, phylogenetic analysis Solanum lycopersicum

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.25 analysis of three-dimensional crystal structure of enzyme DHQD-SDH with shikimate bound in the SDH active site, PDB ID 2GPT. Crystallization of T381G mutant bound with quinate Arabidopsis thaliana

Protein Variants

EC Number Protein Variants Comment Organism
1.1.1.25 additional information absence of the T381 side chain creates sufficient space in the active site to accommodate the quinate C1-hydroxyl. The K385 and D423 catalytic dyad which interacts with C4-OH and participates in proton transfer during the reduction/oxidation of NADP+/NADPH is retained in the T381G mutant Arabidopsis thaliana
1.1.1.25 S338G site-directed mutagenesis, the mutant is not active with quinate like the wild-type Arabidopsis thaliana
1.1.1.25 S338G/T381G site-directed mutagenesis, the double mutant does not show improved enzymatic activity with quinate compared with the T381G mutant Arabidopsis thaliana
1.1.1.25 T381A site-directed mutagenesis, the mutant accepts quinate as a substrate but is much less efficient than the T381G variant Arabidopsis thaliana
1.1.1.25 T381G site-directed mutagenesis, mutant shows increased activity with quinate compared to wild-type, it catalyzes the oxidation of quinate with a turnover rate of 8.8/s and a KM of 3.33 mM Arabidopsis thaliana
1.1.1.25 T381S site-directed mutagenesis, the mutant accepts quinate as a substrate but is much less efficient than the T381G variant Arabidopsis thaliana

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 Arabidopsis thaliana
1.1.1.25 0.548
-
 shikimate pH and temperature not specified in the publication, mutant S338G Arabidopsis thaliana
1.1.1.25 0.604
-
 shikimate pH and temperature not specified in the publication, wild-type enzyme Arabidopsis thaliana
1.1.1.25 0.882
-
 shikimate pH and temperature not specified in the publication, mutant S338G/T381G Arabidopsis thaliana
1.1.1.25 1.539
-
 shikimate pH and temperature not specified in the publication, mutant T381S Arabidopsis thaliana
1.1.1.25 1.613
-
 shikimate pH and temperature not specified in the publication, mutant T381G Arabidopsis thaliana
1.1.1.25 2.512
-
 shikimate pH and temperature not specified in the publication, mutant T381A Arabidopsis thaliana
1.1.1.25 3.33
-
 L-quinate pH and temperature not specified in the publication, mutant T381G Arabidopsis thaliana
1.1.1.25 4.075
-
 L-quinate pH and temperature not specified in the publication, mutant S338G/T381G Arabidopsis thaliana
1.1.1.25 4.485
-
 L-quinate pH and temperature not specified in the publication, mutant T381S Arabidopsis thaliana
1.1.1.25 5.135
-
 L-quinate pH and temperature not specified in the publication, mutant T381A Arabidopsis thaliana
1.1.1.282 0.107
-
 quinate with NAD+, pH and temperature not specified in the publication Nicotiana tabacum
1.1.1.282 0.129
-
 quinate with NAD+, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 0.185
-
 quinate with NAD+, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 0.185
-
 quinate with NADP+, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 0.189
-
 quinate with NAD+, pH and temperature not specified in the publication Brassica napus
1.1.1.282 0.219
-
 NADP+ with quinate, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 0.271
-
 NADP+ with shikimate, pH and temperature not specified in the publication Brassica napus
1.1.1.282 0.314
-
 NAD+ with shikimate, pH and temperature not specified in the publication Nicotiana tabacum
1.1.1.282 0.438
-
 NADP+ with quinate, pH and temperature not specified in the publication Brassica napus
1.1.1.282 0.487
-
 NADP+ with shikimate, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 0.519
-
 NAD+ with shikimate, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 0.519
-
 NADP+ with shikimate, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 0.565
-
 NAD+ with quinate, pH and temperature not specified in the publication Nicotiana tabacum
1.1.1.282 0.635
-
 NAD+ with quinate, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 0.635
-
 NADP+ with quinate, pH and temperature not specified in the publication Solanum lycopersicum

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.1.1.282 chloroplast the NADP+-specific DHQD-QDH from this plant contains a predicted chloroplast-targeting peptide Solanum lycopersicum 9507
-

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.25 shikimate + NADP+ Arabidopsis thaliana
-
 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.282 quinate + NAD+ Nicotiana tabacum
-
 3-dehydroquinate + NADH + H+
-
 r
1.1.1.282 quinate + NAD+ Solanum lycopersicum
-
 3-dehydroquinate + NADH + H+
-
 r
1.1.1.282 quinate + NADP+ Brassica napus
-
 3-dehydroquinate + NADPH + H+
-
 r
1.1.1.282 quinate + NADP+ Brassica rapa
-
 3-dehydroquinate + NADPH + H+
-
 r
1.1.1.282 quinate + NADP+ Solanum lycopersicum
-
 3-dehydroquinate + NADPH + H+
-
 r
1.1.1.282 shikimate + NAD+ Nicotiana tabacum
-
 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.282 shikimate + NAD+ Solanum lycopersicum
-
 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.282 shikimate + NADP+ Brassica napus
-
 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.282 shikimate + NADP+ Brassica rapa
-
 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.282 shikimate + NADP+ Solanum lycopersicum
-
 3-dehydroshikimate + NADPH + H+
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.25 Arabidopsis thaliana Q9SQT8
-
-
1.1.1.282 Brassica napus
-
-
-
1.1.1.282 Brassica rapa
-
-
-
1.1.1.282 Nicotiana tabacum
-
-
-
1.1.1.282 Solanum lycopersicum A0A3Q7H2B2
-
-
1.1.1.282 Solanum lycopersicum A0A3Q7IET9
-
-

Source Tissue

EC Number Source Tissue Comment Organism Textmining
1.1.1.282 flower
-
 Solanum lycopersicum
-
1.1.1.282 fruit
-
 Solanum lycopersicum
-
1.1.1.282 leaf
-
 Solanum lycopersicum
-
1.1.1.282 additional information gene expression analysis Nicotiana tabacum
-
1.1.1.282 additional information gene expression analysis Brassica napus
-
1.1.1.282 additional information gene expression analysis Brassica rapa
-
1.1.1.282 additional information the gene for the NAD+-dependent enzyme shows higher expression in the roots in the later stages of Solanum lycopersicum fruit development and especially during fruit ripening. Unique expression profiles imply that QDH genes for NAD+- and NADP+-specific enzymes, gene expression analysis Solanum lycopersicum
-
1.1.1.282 additional information the NADP+-specific enzyme shows higher expression levels in green tissues, including leaves, green stems and flowers and during the early stages of fruit development, gene expression analysis. The unique expression profiles imply that QDH genes for NAD+- and NADP+-specific enzymes are likely to have distinct physiological roles Solanum lycopersicum
-
1.1.1.282 root
-
 Solanum lycopersicum
-
1.1.1.282 stem green Solanum lycopersicum
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.25 L-quinate + NADP+ activity of T381 enzyme mutants, not of wild-type enzyme, see also EC 1.1.1.282 Arabidopsis thaliana 3-dehydroquinate + NADPH + H+
-
 r
1.1.1.25 shikimate + NADP+
-
 Arabidopsis thaliana 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.282 additional information NAD+-utilizing QDHs are more active with quinate than with shikimate Nicotiana tabacum ?
-
-
1.1.1.282 additional information NAD+-utilizing QDHs are more active with quinate than with shikimate Solanum lycopersicum ?
-
-
1.1.1.282 quinate + NAD+
-
 Nicotiana tabacum 3-dehydroquinate + NADH + H+
-
 r
1.1.1.282 quinate + NAD+
-
 Solanum lycopersicum 3-dehydroquinate + NADH + H+
-
 r
1.1.1.282 quinate + NADP+
-
 Brassica napus 3-dehydroquinate + NADPH + H+
-
 r
1.1.1.282 quinate + NADP+
-
 Brassica rapa 3-dehydroquinate + NADPH + H+
-
 r
1.1.1.282 quinate + NADP+
-
 Solanum lycopersicum 3-dehydroquinate + NADPH + H+
-
 r
1.1.1.282 shikimate + NAD+
-
 Nicotiana tabacum 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.282 shikimate + NAD+
-
 Solanum lycopersicum 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.282 shikimate + NADP+
-
 Brassica napus 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.282 shikimate + NADP+
-
 Brassica rapa 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.282 shikimate + NADP+
-
 Solanum lycopersicum 3-dehydroshikimate + NADPH + H+
-
 r

Synonyms

EC Number Synonyms Comment Organism
1.1.1.25 bifunctional DHQD-SDH/QDH
-
 Arabidopsis thaliana
1.1.1.25 DHQD-SDH
-
 Arabidopsis thaliana
1.1.1.25 EMB3004
-
 Arabidopsis thaliana
1.1.1.25 More cf. EC 4.2.1.10 Arabidopsis thaliana
1.1.1.25 QDH/SDH
-
 Arabidopsis thaliana
1.1.1.282 More cf. EC 4.2.1.10 Solanum lycopersicum
1.1.1.282 NAD+ cofactor-specific QDH
-
 Solanum lycopersicum
1.1.1.282 NADP+ cofactor-specific QDH
-
 Solanum lycopersicum
1.1.1.282 NADP+-specific DHQD-QDH
-
 Solanum lycopersicum
1.1.1.282 QDH
-
 Nicotiana tabacum
1.1.1.282 QDH
-
 Brassica napus
1.1.1.282 QDH
-
 Brassica rapa
1.1.1.282 QDH
-
 Solanum lycopersicum
1.1.1.282 quinate dehydrogenase
-
 Nicotiana tabacum
1.1.1.282 quinate dehydrogenase
-
 Brassica napus
1.1.1.282 quinate dehydrogenase
-
 Brassica rapa
1.1.1.282 quinate dehydrogenase
-
 Solanum lycopersicum

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.25 0.062
-
 L-quinate pH and temperature not specified in the publication, mutant T381S Arabidopsis thaliana
1.1.1.25 0.113
-
 L-quinate pH and temperature not specified in the publication, mutant T381A Arabidopsis thaliana
1.1.1.25 6.7
-
 L-quinate pH and temperature not specified in the publication, mutant S338G/T381G Arabidopsis thaliana
1.1.1.25 8.8
-
 L-quinate pH and temperature not specified in the publication, mutant T381G Arabidopsis thaliana
1.1.1.25 11.8
-
 shikimate pH and temperature not specified in the publication, mutant T381A Arabidopsis thaliana
1.1.1.25 22
-
 shikimate pH and temperature not specified in the publication, mutant S338G/T381G Arabidopsis thaliana
1.1.1.25 24
-
 shikimate pH and temperature not specified in the publication, mutant T381G Arabidopsis thaliana
1.1.1.25 172
-
 shikimate pH and temperature not specified in the publication, mutant T381S Arabidopsis thaliana
1.1.1.25 427
-
 shikimate pH and temperature not specified in the publication, mutant S338G Arabidopsis thaliana
1.1.1.25 516
-
 shikimate pH and temperature not specified in the publication, wild-type enzyme Arabidopsis thaliana
1.1.1.282 0.0018
-
 NADP+ with quinate, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 0.335
-
 NADP+ with shikimate, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 0.493
-
 quinate with NAD+, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 0.74
-
 NAD+ with shikimate, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 3.8
-
 NAD+ with shikimate, pH and temperature not specified in the publication Nicotiana tabacum
1.1.1.282 7
-
 NADP+ with quinate, pH and temperature not specified in the publication Brassica napus
1.1.1.282 8.5
-
 quinate with NAD+, pH and temperature not specified in the publication Brassica napus
1.1.1.282 8.6
-
 NADP+ with shikimate, pH and temperature not specified in the publication Brassica napus
1.1.1.282 9.4
-
 quinate with NAD+, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 10.5
-
 NAD+ with quinate, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 16.2
-
 quinate with NAD+, pH and temperature not specified in the publication Nicotiana tabacum
1.1.1.282 20.8
-
 NAD+ with quinate, pH and temperature not specified in the publication Nicotiana tabacum

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.25 NADP+
-
 Arabidopsis thaliana
1.1.1.25 NADPH
-
 Arabidopsis thaliana
1.1.1.282 NAD+
-
 Nicotiana tabacum
1.1.1.282 NAD+
-
 Solanum lycopersicum
1.1.1.282 NADH
-
 Nicotiana tabacum
1.1.1.282 NADH
-
 Solanum lycopersicum
1.1.1.282 NADP+
-
 Brassica napus
1.1.1.282 NADP+
-
 Brassica rapa
1.1.1.282 NADP+
-
 Solanum lycopersicum
1.1.1.282 NADPH
-
 Brassica napus
1.1.1.282 NADPH
-
 Brassica rapa
1.1.1.282 NADPH
-
 Solanum lycopersicum

General Information

EC Number General Information Comment Organism
1.1.1.25 evolution plant QDHs arose directly from bifunctional dehydroquinate dehydratase-shikimate dehydrogenases (DHQD-SDHs) through different convergent evolutionary events, detailed phylogenetic analysis, overview. Eudicot and conifer QDHs arose early in vascular plant evolution whereas Brassicaceae QDHs emerged late, process of recurrent evolution of QDH. This family of proteins independently evolved NAD+ and NADP+ specificity in eudicots. The acquisition of QDH activity by these proteins is accompanied by the inactivation or functional evolution of the DHQD domain, as verified by enzyme activity assays and as reflected in the loss of key DHQD active site residues Arabidopsis thaliana
1.1.1.25 additional information only four amino acid residues likely to contribute to specificity for one substrate instead of the other, namely S336, S338, T381 and Y550, all of which would be in the direct vicinity of the quinate C1-hydroxyl. Amino acid S336 has previously been shown by mutational analysis to be critical for shikimate binding. The size of the amino acid side chain at position 381 is a key determinant of substrate specificity Arabidopsis thaliana
1.1.1.282 evolution plant QDHs arose directly from bifunctional dehydroquinate dehydratase-shikimate dehydrogenases (DHQD-SDHs) through different convergent evolutionary events, detailed phylogenetic analysis, overview. Eudicot and conifer QDHs arose early in vascular plant evolution whereas Brassicaceae QDHs emerged late, process of recurrent evolution of QDH. This family of proteins independently evolved NAD+ and NADP+ specificity in eudicots. The acquisition of QDH activity by these proteins is accompanied by the inactivation or functional evolution of the DHQD domain, as verified by enzyme activity assays and as reflected in the loss of key DHQD active site residues Nicotiana tabacum
1.1.1.282 evolution plant QDHs arose directly from bifunctional dehydroquinate dehydratase-shikimate dehydrogenases (DHQD-SDHs) through different convergent evolutionary events, detailed phylogenetic analysis, overview. Eudicot and conifer QDHs arose early in vascular plant evolution whereas Brassicaceae QDHs emerged late, process of recurrent evolution of QDH. This family of proteins independently evolved NAD+ and NADP+ specificity in eudicots. The acquisition of QDH activity by these proteins is accompanied by the inactivation or functional evolution of the DHQD domain, as verified by enzyme activity assays and as reflected in the loss of key DHQD active site residues Brassica napus
1.1.1.282 evolution plant QDHs arose directly from bifunctional dehydroquinate dehydratase-shikimate dehydrogenases (DHQD-SDHs) through different convergent evolutionary events, detailed phylogenetic analysis, overview. Eudicot and conifer QDHs arose early in vascular plant evolution whereas Brassicaceae QDHs emerged late, process of recurrent evolution of QDH. This family of proteins independently evolved NAD+ and NADP+ specificity in eudicots. The acquisition of QDH activity by these proteins is accompanied by the inactivation or functional evolution of the DHQD domain, as verified by enzyme activity assays and as reflected in the loss of key DHQD active site residues Brassica rapa
1.1.1.282 evolution plant QDHs arose directly from bifunctional dehydroquinate dehydratase-shikimate dehydrogenases (DHQD-SDHs) through different convergent evolutionary events, detailed phylogenetic analysis, overview. Eudicot and conifer QDHs arose early in vascular plant evolution whereas Brassicaceae QDHs emerged late, process of recurrent evolution of QDH. This family of proteins independently evolved NAD+ and NADP+ specificity in eudicots. The acquisition of QDH activity by these proteins is accompanied by the inactivation or functional evolution of the DHQD domain, as verified by enzyme activity assays and as reflected in the loss of key DHQD active site residues Solanum lycopersicum
1.1.1.282 additional information only four amino acid residues likely to contribute to specificity for one substrate instead of the other, namely S336, S338, T381 and Y550, all of which would be in the direct vicinity of the quinate C1-hydroxyl. Amino acid S336 has previously been shown by mutational analysis to be critical for shikimate binding. The size of the amino acid side chain at position 381 is a key determinant of substrate specificity Nicotiana tabacum
1.1.1.282 additional information only four amino acid residues likely to contribute to specificity for one substrate instead of the other, namely S336, S338, T381 and Y550, all of which would be in the direct vicinity of the quinate C1-hydroxyl. Amino acid S336 has previously been shown by mutational analysis to be critical for shikimate binding. The size of the amino acid side chain at position 381 is a key determinant of substrate specificity Brassica napus
1.1.1.282 additional information only four amino acid residues likely to contribute to specificity for one substrate instead of the other, namely S336, S338, T381 and Y550, all of which would be in the direct vicinity of the quinate C1-hydroxyl. Amino acid S336 has previously been shown by mutational analysis to be critical for shikimate binding. The size of the amino acid side chain at position 381 is a key determinant of substrate specificity Brassica rapa
1.1.1.282 additional information only four amino acid residues likely to contribute to specificity for one substrate instead of the other, namely S336, S338, T381 and Y550, all of which would be in the direct vicinity of the quinate C1-hydroxyl. Amino acid S336 has previously been shown by mutational analysis to be critical for shikimate binding. The size of the amino acid side chain at position 381 is a key determinant of substrate specificity Solanum lycopersicum

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.1.1.25 0.014
-
 L-quinate pH and temperature not specified in the publication, mutant T381S Arabidopsis thaliana
1.1.1.25 0.022
-
 L-quinate pH and temperature not specified in the publication, mutant T381A Arabidopsis thaliana
1.1.1.25 1.64
-
 L-quinate pH and temperature not specified in the publication, mutant S338G/T381G Arabidopsis thaliana
1.1.1.25 2.64
-
 L-quinate pH and temperature not specified in the publication, mutant T381G Arabidopsis thaliana
1.1.1.25 4.7
-
 shikimate pH and temperature not specified in the publication, mutant T381A Arabidopsis thaliana
1.1.1.25 14.9
-
 shikimate pH and temperature not specified in the publication, mutant T381G Arabidopsis thaliana
1.1.1.25 24.9
-
 shikimate pH and temperature not specified in the publication, mutant S338G/T381G Arabidopsis thaliana
1.1.1.25 111.8
-
 shikimate pH and temperature not specified in the publication, mutant T381S Arabidopsis thaliana
1.1.1.25 779.2
-
 shikimate pH and temperature not specified in the publication, mutant S338G Arabidopsis thaliana
1.1.1.25 854.3
-
 shikimate pH and temperature not specified in the publication, wild-type enzyme Arabidopsis thaliana
1.1.1.282 0.008
-
 NADP+ with quinate, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 0.688
-
 NADP+ with shikimate, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 1.43
-
 NAD+ with shikimate, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 3.82
-
 quinate with NAD+, pH and temperature not specified in the publication Brassica rapa
1.1.1.282 12.1
-
 NAD+ with shikimate, pH and temperature not specified in the publication Nicotiana tabacum
1.1.1.282 15.98
-
 NADP+ with quinate, pH and temperature not specified in the publication Brassica napus
1.1.1.282 16.5
-
 NAD+ with quinate, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 31.73
-
 NADP+ with shikimate, pH and temperature not specified in the publication Brassica napus
1.1.1.282 36.8
-
 NAD+ with quinate, pH and temperature not specified in the publication Nicotiana tabacum
1.1.1.282 44.97
-
 quinate with NAD+, pH and temperature not specified in the publication Brassica napus
1.1.1.282 50.8
-
 quinate with NAD+, pH and temperature not specified in the publication Solanum lycopersicum
1.1.1.282 151.4
-
 quinate with NAD+, pH and temperature not specified in the publication Nicotiana tabacum