Literature summary for 2.7.1.71 extracted from

Cheng, W.C.; Chen, Y.F.; Wang, H.J.; Hsu, K.C.; Lin, S.C.; Chen, T.J.; Yang, J.M.; Wang, W.C.
Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism (2012), PLoS ONE, 7, e33481.

Crystallization (Commentary)

Crystallization (Comment)	Organism
wild-type dimeric enzyme, wild-type enzyme in complex with products ADP and shikimate 3-phosphate, enzyme mutant R57A, and enzyme mutant E114A in complex with selective inhibitor NSC162535, hanging drop vapour ddiffusion metho, 50 mg/ml protein in 40 mM Tris-HCl, pH 7.0, containing 100 mM NaCl mixed with an equal volume of reservoir solution and equilibrated against 0.06 ml of reservoir solution, containing 0.2 M Li2SO4, 30% w/v PEG 8000, and 0.1 M sodium acetate, pH 6.5 for the apo-enzyme, or containing 0.1 M HEPES sodium salt, pH 7.5, 0.1 M sodium acetate, 18% w/v PEG 8000, 2% w/v 2-propanol, and 5 mM shikimate and 5 mM MgATP for the product complex enzyme, or containing 0.1 M HEPES sodium salt, pH 8.0, 8% w/v 2-propanol and 18% w/v PEG 4000 for enzyme mutant R57A, or containing 0.1 M HEPES sodium salt, pH 6.7, and 1.2 M potassium sodium tartrate tetrahydrate for the enzyme mutant E114A with inhibitor, X-ray diffraction structure determination and analysis at 1.8 A, 2.3 A, 2.4 A, and 2.53 A resolution, respectively, molecular replacement	Helicobacter pylori

Crystallization (Comment)

Organism

wild-type dimeric enzyme, wild-type enzyme in complex with products ADP and shikimate 3-phosphate, enzyme mutant R57A, and enzyme mutant E114A in complex with selective inhibitor NSC162535, hanging drop vapour ddiffusion metho, 50 mg/ml protein in 40 mM Tris-HCl, pH 7.0, containing 100 mM NaCl mixed with an equal volume of reservoir solution and equilibrated against 0.06 ml of reservoir solution, containing 0.2 M Li2SO4, 30% w/v PEG 8000, and 0.1 M sodium acetate, pH 6.5 for the apo-enzyme, or containing 0.1 M HEPES sodium salt, pH 7.5, 0.1 M sodium acetate, 18% w/v PEG 8000, 2% w/v 2-propanol, and 5 mM shikimate and 5 mM MgATP for the product complex enzyme, or containing 0.1 M HEPES sodium salt, pH 8.0, 8% w/v 2-propanol and 18% w/v PEG 4000 for enzyme mutant R57A, or containing 0.1 M HEPES sodium salt, pH 6.7, and 1.2 M potassium sodium tartrate tetrahydrate for the enzyme mutant E114A with inhibitor, X-ray diffraction structure determination and analysis at 1.8 A, 2.3 A, 2.4 A, and 2.53 A resolution, respectively, molecular replacement

Helicobacter pylori

Protein Variants

Protein Variants	Comment	Organism
D33A	site-directed mutagensis, inactive mutant	Helicobacter pylori
D33E	site-directed mutagensis, inactive mutant	Helicobacter pylori
E114A	site-directed mutagensis, the mutant shows 82% of wlld-type activity	Helicobacter pylori
F48A	site-directed mutagensis, inactive mutant	Helicobacter pylori
F48Y	site-directed mutagensis, the mutant shows 40% of wlld-type activity	Helicobacter pylori
M10A	site-directed mutagensis, the mutant shows 38% of wlld-type activity	Helicobacter pylori
R116A	site-directed mutagensis, inactive mutant	Helicobacter pylori
R116K	site-directed mutagensis, inactive mutant	Helicobacter pylori
R132A	site-directed mutagensis, the mutant shows 5% of wlld-type activity	Helicobacter pylori
R132K	site-directed mutagensis, inactive mutant	Helicobacter pylori
R57A	site-directed mutagensis, the mutant shows 2% of wlld-type activity	Helicobacter pylori
R57K	site-directed mutagensis, the mutant shows 2% of wlld-type activity	Helicobacter pylori

General Stability

General Stability	Organism
differential scanning calorimetry experiments for evaluaton of the stability and unfolding of each of the enzyme mutants, overview	Helicobacter pylori

Inhibitors

Inhibitors	Comment	Organism	Structure
NSC162535	selective inhibitor, identification and binding analysis with enzyme mutant E144A by virtual docking analysis, isothermal titration calorimetry, and crystals structure analysis revealing an induced-fit mechanism, inactivation mechanism, detailed overview. Binding kinetics of wild-type and mutant enzymes	Helicobacter pylori

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.039	-	shikimate	enzyme mutant E114A, pH 7.5, 25°C	Helicobacter pylori
0.06	-	shikimate	wild-type enzyme, pH 7.5, 25°C	Helicobacter pylori
0.101	-	ATP	wild-type enzyme, pH 7.5, 25°C	Helicobacter pylori
0.101	-	ATP	enzyme mutant M10A, pH 7.5, 25°C	Helicobacter pylori
0.135	-	shikimate	enzyme mutant M10A, pH 7.5, 25°C	Helicobacter pylori
0.143	-	ATP	enzyme mutant E114A, pH 7.5, 25°C	Helicobacter pylori
0.231	-	ATP	enzyme mutant F48Y, pH 7.5, 25°C	Helicobacter pylori
0.291	-	shikimate	enzyme mutant F48Y, pH 7.5, 25°C	Helicobacter pylori

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Helicobacter pylori

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + shikimate	Helicobacter pylori	-	ADP + 3-phosphoshikimate	-	?

Organism

Organism	UniProt	Comment	Textmining
Helicobacter pylori	P56073	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
ATP + shikimate	-	Helicobacter pylori	ADP + 3-phosphoshikimate	-	?

Subunits

Subunits	Comment	Organism
dimer	detailed structure-activity relationship analysis, overview	Helicobacter pylori

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Helicobacter pylori

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Helicobacter pylori

Cofactor

Cofactor	Comment	Organism	Structure
ATP	-	Helicobacter pylori

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor	Structure
0.0049	-	pH 7.5, 25°C	Helicobacter pylori	NSC162535

General Information

General Information	Comment	Organism
metabolism	shikimate kinase catalyzes the fifth step of the shikimate pathway for biosynthesis of aromatic amino acids	Helicobacter pylori
additional information	detailed structure-activity relationship analysis, overview. The critical conserved residues D33, F48, R57, R116, and R132 interact with shikimate. A characteristic three-layer architecture and a conformationally elastic region consisting of F48, R57, R116, and R132 are occupied by shikimate	Helicobacter pylori