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4.2.1.10: 3-dehydroquinate dehydratase

This is an abbreviated version!
For detailed information about 3-dehydroquinate dehydratase, go to the full flat file.

Word Map on EC 4.2.1.10

Reaction

3-dehydroquinate
=
3-dehydroshikimate
 +
H2O

Synonyms

3-dehydroquinase, 3-dehydroquinate dehydratase, 3-dehydroquinate dehydratase /shikimate dehydrogenase isoform 1, 3-dehydroquinate dehydratase /shikimate dehydrogenase isoform 2, 3-dehydroquinate dehydratase/shikimate dehydrogenase, 3-DHQase, 5-dehydroquinase, 5-dehydroquinate dehydratase, 5-dehydroquinate hydro-lyase, AfDQ, aroD, AroQ, bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplast, dehydratase, 3-dehydroquinate, dehydroquinase, dehydroquinate dehydratase, dehydroquinate dehydratase-shikimate dehydrogenase, dehydroquinate synthase, DHD/SHD, DHQ synthase, DHQ-SDH, DHQ-SDH protein, DHQ/SDH, DHQ1, DHQ2, DHQase, DHQase I, DHQase-SORase, DHQD, DHQS, DQD, EC 4.2.1.10, EcDQD/SDH1, EcDQD/SDH2, mDQD, membrane-bound 3-dehydroquinate dehydratase, More, MtDHQase, NtDHD/SHD-1, NtDHD/SHD-2, pDQD, sDQD, SVCR3, type I 3-dehydroquinate dehydratase, Type I dehydroquinase, type I dehydroquinate dehydratase, Type I DHQase, type I DHQD, type II 3-dehydroquinate dehydratase, Type II dehydroquinase, Type II DHQase

ECTree

     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.1 Hydro-lyases
                4.2.1.10 3-dehydroquinate dehydratase

Crystallization

Crystallization on EC 4.2.1.10 - 3-dehydroquinate dehydratase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
to 2.0 A resolution, monoclinic space group P21 with cell dimensions a = 82.3, b = 95.3, c = 132.3 A and beta = 95.7°. The protein molecules form a dodecamer with four trimers arranged in a tetrahedral manner. The classical lid adopts an open conformation although a sulfate ion is observed in the substrate binding site
crystals obtained in space and on earth using the counter-diffusion technique
-
the enzyme is co-crystallized with the ligand TLA(C4H6O6) or L(+)-tartaric acid, sitting drop vapor diffusion method, using 30% (w/v) polyethylene glycol 4000, 0.2 M ammonium acetate and 0.1 M citrate, pH 5.6
-
vapor diffusion hanging-drop technique, crystal structure of DHQ-SDH with shikimate bound at the SDH site and tartrate at the DHQ site
the structure of the 3-dehydroquinate dehydratase dimer is determined at 2.33 A resolution
wild-type enzyme post-dehydration covalent intermediate, from 100 mM Tris, pH 8.5, 30% w/v PEG 500, X-ray diffraction structure determination and analysis at 2.20 A resolution
-
to 2.2 A resolution
DHQ2 in complex with (2R)-2-p-methoxybenzyl-3-dehydroquinic acid, sitting drop vapour diffusion method, 20 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 1 mM 2-mercaptoethanol, 1 mM EDTA, and 200 mM NaCl, with addition of (2R)-2-p-methoxybenzyl-3-dehydroquinic acid at 0.25 M in methanol and added at a ratio of 1:20 v/v, mixing of 0.002 ml protein solution with 0.002 ml reservoir solution containing 31% w/v PEG 4000 and 0.1 M sodium citrate, pH 5.0, and equilibation against 0.15 ml reservoir solution, room temperature, X-ray diffraction structure determination and analysis at 2.4-2.5 A resolution, modelling
DHQ2 in complex with inhibitors (4R,6R,7S)-4,6,7-trihydroxy-2-[(1Z)-prop-1-en-1-yl]-4,5,6,7-tetrahydro-1-benzothiophene-4-carboxylic acid and (4R,6R,7S)-2-(1-cyclopropylethyl)-4,6,7-trihydroxy-4,5,6,7-tetrahydro-1-benzothiophene-4-carboxylic acid, X-ray diffraction structure determination and analysis at 1.95 and 1.85 A resolution, respectively
-
DHQase-AH9095 complex
-
hanging drop vapor diffusion method
-
molecular dynamics simulations and comparison of DHQ2 enzymes from Mycobacterium tuberculosis and Helicobacter pylori. The rate-determining step involves the formation of an enolate intermediate. The enolate and transition state of the key step is more efficiently stabilized in Mycobacterium tuberculosis DHQ2, mainly by the essential residues Tyr24 and Arg19. A water molecule, which is absent in Mycobacterium tuberculosis DHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in Helicobacter pylori DHQ2, destabilizes both the transition state and the enolate intermediate
sitting drop vapor diffusion method, crystal structures of type II dehydroquinase with the inhibitors 2,3-anhydroquinate, citrate or N-tetrazol-5-yl-9-oxo-9H-xanthene-2-sulfonamide
sitting drop vapor diffusion method, using 26% (w/v) polyethyleneglycol 4000 and 0.1 M 2-(N-morpholino)ethanesulfonic acid sodium hydroxide, pH 5.0
the crystal structure of dehydroquinate synthase complexed with NAD is determined at 2.4 A resolution
-
truncated form of type II DHQase
-
crystal structure in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, at 1.5 A. Residues Gln236, Pro234 and Ala233 are located in the flexible substrate-covering loop. Gln236 is responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 is important in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis
-
DHQ2 in complex with (2R)-2-p-methoxybenzyl-3-dehydroquinic acid, sitting drop vapour diffusion method, 20 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 1 mM 2-mercaptoethanol, 1 mM EDTA, and 200 mM NaCl, with addition of (2R)-2-p-methoxybenzyl-3-dehydroquinic acid at 0.25 M in methanol and added at a ratio of 1:20 v/v, mixing of 0.002 ml protein solution with 0.002 ml reservoir solution containing 32% v/v 2-methyl-2,4-pentanediol, 0.3 M ammonium sulfate and 0.1 M HEPES, pH 7.5, and equilibation against 0.15 ml reservoir solution, room temperature, X-ray diffraction structure determination and analysis at 2.4-2.5 A resolution, modelling
-
enzyme in complex with product 3-dehydroshikimate, X-ray diffraction structure determination and analysis
hanging drop vapor diffusion method
in complex with inhibitors 5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid and 3,4-dihydroxy-5-((3-nitrobenzyl)oxy)benzoic acid
in complex with inhibitors, using 32% (v/v) 2-methyl-2,4-pentanediol, 0.3 M ammonium sulfate and 0.1 M 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid sodium salt, pH 7.5
molecular dynamics simulations and comparison of DHQ2 enzymes from Mycobacterium tuberculosis and Helicobacter pylori. The rate-determining step involves the formation of an enolate intermediate. The enolate and transition state of the key step is more efficiently stabilized in Mycobacterium tuberculosis DHQ2, mainly by the essential residues Tyr24 and Arg19. A water molecule, which is absent in Mycobacterium tuberculosis DHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in Helicobacter pylori DHQ2, destabilizes both the transition state and the enolate intermediate
study on the crystallographic structures of DHQD in complex with competitive inhibitors, and application of supervised machine learning techniques elaborate a robust DHQD-targeted model to predict binding affinity. The prevalence of intermolecular electrostatic interactions between DHQD and competitive inhibitors is of great importance for the binding affinity against the enzyme
to 1.74 A resolution, space group F23, with unit-cell parameters a = b = c = 125.39 A
in complex with quinate and shikimate, sitting drop vapor diffusion method, using 0.01 M nickel chloride, 0.1 M Tris (pH 8.5), and 20% poly(ethylene glycol) monomethyl ether 2000
mutant enzymes E86A and E86Q, sitting drop vapor diffusion method, using 0.2 M sodium chloride and 20% (w/v) PEG 3350 (unliganded structure), 0.19 M sodium chloride and 17.9% (w/v) PEG 3350 (cocrystallized E86A-3-dehydroshikimate complex), 0.1 M MIB buffer (pH 9.0) and 25% (w/v) PEG 1500 (soaked E86A-3-dehydroshikimate complex)
purified recombinant DHQD by sitting drop vaour diffusion method, generation of three different crystal forms, the protein solution contains 500 mM NaCl and 10 mM Tris-HCl, pH 8.3, mixing of protein and reservoir solution in a 1:1 ratio at room temperature, the reservoir solutions contain: 200 mM MgCl2 and 20% PEG 3350, or 170 mM NH4OAc, pH 4.6, 25.5% PEG 4000, and 15% glycerol, or 200 mM MgCl2, 100 mM Tris, pH 8.5, and 20% PEG 3350 for the wild-type enzyme in open or in closed conformation of for the mutant Q236A, X-ray diffraction structure determination and analysis at 1.03-1.93 A resolution. The Q236A enzyme crystallized in another crystal form that diffracts to a significantly higher resolution than any of the wild-type crystals
wild-type enzyme pre-dehydration covalent intermediate, and mutant K170M in complex with 3-dehydroquinate, crystallization of the wild-type enzyme from 170 mM NH4OAc, pH 4.6, 25.5% w/v PEG 4000, 15% v/v glycerol, the mutant is crystallized from 50 mM K2PO4, pH 6.0, 20% w/v PEG 8000, X-ray diffraction structure determination and analysis at 1.6-1.95 A resolution
crystal structure in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, at 1.5 A. Residues Gln236, Pro234 and Ala233 are located in the flexible substrate-covering loop. Gln236 is responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 is important in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis
in complex with inhibitor (3S,5R,7R,8S)-5,7,8-trihydroxy-1-oxaspiro[2.5]octane-5-carboxylic acid, to 1.4 A resolution. The ligand is covalently attached to the essential Lys170 residue by formation of a stable Schiff base
sitting-drop vapor-diffusion method
-
large DHQase–CA1 inhibitor complex