1.1.1.25: shikimate dehydrogenase

This is an abbreviated version, for detailed information about shikimate dehydrogenase, go to the full flat file.

Reaction

shikimate
+
NADP+
=
3-dehydroshikimate
+
NADPH
+
H+

Synonyms

3-dehydroquinate dehydratase/shikimate dehydrogenase, 5-dehydroshikimate reductase, ael1, Af2327, AroE, cgR_0495, cgR_1677, dehydroquinate dehydratase-shikimate dehydrogenase, dehydroshikimic reductase, DHD/SHD, DHQ-SDH, HI0607, More, MtbSD, NADP-dependent shikimate dehydrogenase, qsuD, rifI, SD, SDH, sdhL, shikimate 5-dehydrogenase, shikimate dehydrogenase, shikimate oxidoreductase, shikimate:NADP oxidoreductase, shikimate:NADP+ 5-oxidoreductase, SKDH, tm0346

ECTree

     1 Oxidoreductases
         1.1 Acting on the CH-OH group of donors
             1.1.1 With NAD+ or NADP+ as acceptor
                1.1.1.25 shikimate dehydrogenase

Crystallization

Crystallization on EC 1.1.1.25 - shikimate dehydrogenase

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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
apo-enzyme and in complex with both shikimate and NADP+, which assumes the closed conformation
in complex with shikimate, and in ternary complex with shikimate and NADP+
-
purified native and selenomethionine-labeled DELTA88DHQ-SDH complexed with shikimate, hanging drop vapour diffusion method, 10 mg/ml protein in 1 mM shikimate mixed with equal volume of reservoir solution containing 0.4 M potassium sodium tartrate tetrahydrate, 0.1 M tri-sodium dihydrate, pH 5.6, and 2.8 M ammonium sulfate, X-ray diffraction structure determination and analysi at 1.95-2.2 A resolution
-
crystallized at 23°C using ammonium sulfate as a precipitant. Crystals grown in the presence of NADP+ diffract to 2.8 A resolution and belong to the trigonal space group P3(2)21 (or P3(2)21), with unit-cell parameters a = 111.3, b = 111.3, c = 76.2 A; in complex with NADP+, to 2.8 A resolution. Crystal belong to space group P3221
purified recombinant enzyme, sitting drop vapour diffusion method, 3.75 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 0.5 M NaCl, 1 mM NaN3, and 20% v/v glycerol, the reservoir solution contains 0.1 M sodium acetate, pH 4.6, 0.2 M NaCl, and 20% v/v precipitant 2,4-methylenepentanediol, 0.002 ml of protein, reservoir and 0.002 mM NADH solutions are mixed at 20°C, about 5 months, formation of rod- and needle-shaped crystals, X-ray diffraction structure determination and analysis at 1.64 A resolution
-
; purified recombinant enzyme, 20 mg/ml in 10 mM Tris-HCl, pH 7.6, 0.4 mM DTT, and 2.5 mM NADPH, 20°C, sitting-drop vapour-diffusion method, reservoir solution contains 1.65 M ammonium sulfate, 100 mM cacodylate buffer, pH 5.8, 1.5 ml of protein solution is mixed with an equal volume of reservoir solution, 10-12 days, cryoprotection with 20% v/v glycerol, X-ray diffraction structure determination and analysis at 2.3 A resolution
-
catalytic domain with open twisted alpha/beta motif plus NADPH binding domain with typical Rossman fold; wild-type and selenomethionine-labeled enzyme, free and in complex with NADPH, sitting drop vapour diffusion method, 10 mg/m protein, with or without 5 mM NADPH, mixture in a ratio of 1:1 with crystallization solution containing 1.0 M sodium citrate, and 0.1 M 2-(cyclohexylamino)ethanesulfonic acid (CHES), pH 8.8, for the free enzyme, and 12% PEG 8000, 0.15 M calcium acetate, pH 7.8, and 0.1 M imidazole for the selenomethionine-labeled enzyme, 4°C, X-ray diffraction structure determination and analysis at 2.4 A and 1.95 A, respectively, structure modeling
purified recombinant wild-type and selenomethionine-labeled paralogue HI0607, hanging drop vapour diffusion method, 0.001 ml protein solution containing 20 mg/ml protein mixed with equal volume of reservoir solution containing 0.1 M sodium acetate, pH 4.6, 2.0 M NaCl, and 10% v/v PEG 400, X-ray diffraction structure determination and analysis at 1.75 A resolution
-
in complex with NADP+, compact alpha/beta sandwich with two domains for binding substrate and cofactor, resp.; purified recombinant AroE bound to cofactor NADP+, hanging drop vapour diffusion method at 25°C, 10 mg/ml protein in 20 mM HEPES, pH 7.1, and 0.1 M KCl, is mixed with reservoir solution containing 20 mM HEPES, pH 7.1, 20% PEG 3350, and 0.2 M ammonium fluoride, cryoprotection with 15% glycerol, X-ray diffraction structure determination and analysis at 2.35 A resolution
homology modeling and circular dichroism study. NADP+ binding results in small conformational changes
-
at 4°C, using the hanging-drop vapor-diffusion method. SDH both in its ligand-free form and in complex with shikimate. Overall structure of apo-SDH is basically identical to that of the shikimate-SDH complex, both structures contain one molecule per asymmetric unit. Overall folding of SDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211 does not interact with shikimate in the binary SDH-shikimate complex structure. The main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SDH is less conserved. The long helix specifically recognizing the adenine ribose phosphate is substituted with a short 310 helix in the NADP-binding domain. The interdomain angle of SDH is the widest among all known SDH structures, indicating an inactive open state of the SDH structure. Thus, a closing process may occur upon NADP+ binding to bring the cofactor close to the substrate for catalysis
determination of the crystal structure at 1.45 A by molecular replacement. The protein shows a monomeric architecture. The overall structure comprises the N-terminal alpha/beta sandwich domain for substrate binding and the C-terminal domain for NADP binding.the enzyme is in a tightly closed conf ormation, which should be open for catalysis. Four ammonium sulfate ions were identified in the structure. They are located in the active site and appear to mimic the role of the substrate in terms of the enzyme activity and stability
-
to 1.45 A resolution. Space group P212121
-
ligand-free form, binary complexes with NADP+ or substrate shikimate, and ternary complex with both NADP+ and shikimate. Structures of the closed subunits with and without NADP(H) show no significant difference. Residues K64 and D100 are involved in hydride transfer