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2.5.1.19: 3-phosphoshikimate 1-carboxyvinyltransferase

This is an abbreviated version!
For detailed information about 3-phosphoshikimate 1-carboxyvinyltransferase, go to the full flat file.

Word Map on EC 2.5.1.19

Reaction

phosphoenolpyruvate
+
3-phosphoshikimate
=
phosphate
 +
5-O-(1-carboxyvinyl)-3-phosphoshikimate

Synonyms

3-enolpyruvylshikimate 5-phosphate synthase, 3-enolpyruvylshikimic acid-5-phosphate synthetase, 3-phosphoshikimate 1-carboxyvinyl-transferase, 3-phosphoshikimate 1-carboxyvinyltransferase, 3-phosphoshikimate-1-carboxyvinyl-transferase, 5'-enolpyruvylshikimate-3-phosphate synthase, 5-enol pyruvylshikimate 3-phosphate synthase, 5-enol-pyruvyl-shikimate-3-phosphate synthase, 5-enol-pyruvylshikimate 3-phosphate synthase, 5-enol-pyruvylshikimate-3-phosphate synthase, 5-enolpyruvyl-3-phosphoshikimate synthase, 5-enolpyruvylshikimate 3-phosphate synthase, 5-enolpyruvylshikimate-3-phosphate synthase, 5-enolpyruvylshikimate-3-phosphate synthetase, 5-enolpyruvylshikimate-3-phosphoric acid synthase, 5-enolpyruvylshikimate-3phosphate synthase, 5-enolpyruvylshikimic acid-3-phosphate synthase, 5-enopyruvylshikimate-3-phosphate synthase, 5-enoylpyruvylshikimate 3-phosphate synthase, 5-enoylpyruvylshikimate-3-phosphate synthase, A1501 EPSPS, AM79, AroA, AroA(1398), AroA(A1501), AroA1398, CaEPSPS, cp4 epsps, DsaroA, Dunaliella salina 5-enolpyruvylshikimate-3-phosphate synthase, Dunaliella salina EPSP synthase, E. coli EPSPS, EcaroA, enolpyruvylshikimate 3-phosphate synthase, enolpyruvylshikimate phosphate synthase, enolpyruvylshikimate-3-phosphate synthase, EPSP synhthase, EPSP synthase, EPSPS, G2 5-enolpyruvyl shikimate 3-phosphate synthase, G2 EPSPS, GR79Ms, maize EPSP synthase, maize EPSPS, mEPSPS, More, Mt EPSPS, Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase, Potri.002G146400, StaroA, synthase, 5-enolpyruvoylshikimate 3-phosphate

ECTree

     2 Transferases
         2.5 Transferring alkyl or aryl groups, other than methyl groups
             2.5.1 Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)
                2.5.1.19 3-phosphoshikimate 1-carboxyvinyltransferase

Crystallization

Crystallization on EC 2.5.1.19 - 3-phosphoshikimate 1-carboxyvinyltransferase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
microbatch under oil method, using 100 mM bis-Tris propane pH 7.0, 100 mM potassium bromide, 40% (w/v) PEG 8000
-
wild-type in presence of 5 mM inhibitor (3R,4S,5R)-5-[(2R)-1,1-difluoro-3-hydroxy-3-oxo-2-phosphonooxy-propan-2-yl]oxy-4-hydroxy-3-phosphonooxy-cyclohexene-1-carboxylic acid (2F-TI, PDB: 2PQB) or (3R,4S,5R)-4-hydroxy-5-[(2R)-1-hydroxy-1-oxo-2-phosphono-propan-2-yl]oxy-3-phosphonooxy-cyclohexene-1-carboxylic acid (RP-TI, PDB: 2PQC), and mutant A100G in presence of 5 mM inhibitor 2F-TI (PDB: 2PQD): 2F-TI-binding induces only slight shift of Glu354 side chain but substantial conformational change of 2F-TI molecule that is independent of residue 100 but mediated by residue Thr101 and due to rigidity of active site, RP-TI-binding induces slight movement of Glu354 side chain and occurs via salt bridge with residue Arg128 but does not alter enzyme’s backbone compared to the shikimate 3-phosphate bound enzyme, crystals: space group P2(1), unit cell parameters: a: 62.8-63.4, b: 44.9-45.0, c: 77.1-77.6, beta: 106.1-106.3°, hanging-drop vapour-diffusion, ammonium sulfate conditions, molecular replacement using PDB: 2GG6 as model, co-crystallization with (3R,4S,5R)-4-hydroxy-5-[(2S)-1-hydroxy-1-oxo-2-phosphono-propan-2-yl]oxy-3-phosphonooxy-cyclohexene-1-carboxylic acid (SP-TI) not succeeded, docking of SP-TI into substrate- or inhibitor-bound structures indicates low electrostatic interactions between enzyme and inhibitor
molecular docking using known structures of EPSPS in complex with (R)-phosphonate analogue of the tetrahedral reaction intermediate
-
three-dimensional structure modeling of mutations P318R and M425T. Results indicate that the enzyme's lower hemisphere’s upper surface is possibly another important region for glyphosate resistance
hanging drop vapor diffusion method, using 0.1 M Bis-Tris pH 6.5, 0.2 M NaCl, 20% (w/v) PEG 3350, and 5-10% (v/v) glycerol
sitting drop vapor diffusion method, using either 0.1 M trisodium citrate (pH 4.0) and 0.8 M ammonium sulfate (unliganded-open enzyme form) or 4.3 M NaCl and 0.1 M HEPES (pH 7.5) (unliganded-closed enzyme form) or 0.1 M Bis-Tris (pH 6.5) and 25% (w/v) PEG3350 (in complex with 3-phosphoshikimate and glyphosate) or 0.2 M ammonium sulfate, 0.1 M HEPES (pH 7.5), and 25% (w/v) PEG 3350 (in complex with K+, phosphate and 3-phosphoshikimate)
enzyme complexed with inhibitor (3R,4S,5R)-5-((S)-1-carboxy-1-phosphono-ethoxy)-4-hydroxy-3-phosphonooxy-cyclohex-1-enecarboxylic acid or with inhibitor (3R,4S,5R)-5-((R)-1-carboxy-1-phosphono-ethoxy)-4-hydroxy-3-phosphonooxy-cyclohex-1-enecarboxylic acid, 100 mg/ml recombinant enzyme in 2.5 M sodium formate with 10 mM inhibitor, hanging drop vapour diffusion method, 19°C, X-ray diffraction at -180°C using the rotation method on single flash-frozen crystals, structure determination and analysis at 1.5 and 1.9 A resolution, respectively
enzyme in complex with shikimate/glyphosate at 1.5 A resolution
in presence of 10 mM inhibitor (3R,4S,5R)-5-[(2R)-1,1-difluoro-3-hydroxy-3-oxo-2-phosphonooxy-propan-2-yl]oxy-4-hydroxy-3-phosphonooxy-cyclohexene-1-carboxylic acid (2F-TI, PDB: 2PQ9), 2F-TI-binding induces large conformational change of Glu341 side chain compared to TI-binding, crystals: space group P2(1)2(1)2(1), unit cell parameters: a: 58.2, b: 85.1, c: 87.6, beta: 90°, hanging-drop vapour-diffusion, sodium format conditions, molecular replacement using PDB: 1G6S as model
mutants P101S and P101L in complex with shikimate 3-phosphate and with or without inhibitor glyphosate, long-range structural change in glyphosate binding site compared to wild-type, Gly96 and Thr97 are shifted towards the glyphosate-binding site, which gets slightly narrowed, crystals: space group: P2(1)2(1)2(1), unit cell parameters: a: 57.6-57.8, b: 85.1-85.6, c: 87.9-88.3, beta: 90°, hanging-drop vapour-diffusion, protein solution (37.5 mg/ml, 5 mM inhibitor and/or 5 mM shikimate 3-phosphate), 19°C, molecular replacement using PDB: 1G6S as model
purified recombinant wild-type and mutant enzymes in complex with the substrates, at 19°C, from 4 M sodium formate in presence of 5 mM 3-phosphoshikimate and 5 mM phosphoenolpyruvate, X-ray diffraction structure determination and analysis at 1.6 A resolution
semiempirical molecular modelling using, among others, the crystal structure of EPSPS mutant D313A (PDB: 1Q36) as model for assignment of protonation states of all basic amino acids in the active site: in the enzyme-tetrahedral reaction intermediate (TI) complex is residue His385 in a neutral form (with protonated epsilon-N atom) while residues Lys22, Lys340 and Lys411 are protonated, hydrogen bonds occur between Lys22 and the carboxylate oxygen atom of the phosphoenolpyruvate moiety of the TI, Asp313 has only minor effects on TI positioning within the active site but mediates as a base the attack of the TI C4-hydroxyl group on the TI methyl group prior to EPSP formation
using the hanging drop, vapor-diffusion method in the presence of 5 mM 3-phosphoshikimate
restrained-based, molecular modelling; open conformation model of apoenzyme generated based on coordinates from PDB: 2BJB (MtEPSPS), closed conformation model of enzyme/3-phosphoshikimate/glyphosate complex generated based on PDB: 1G6S
molecular modelling, two similar globular, inside-out alpha-beta-barrel domains connected by a two-stranded hinge, substrates bind at the inter-domain cleft
-
sitting drop vapor diffusion method, using 0.2 M MgCl, 0.1 M HEPES (pH 7.5), and 25% (w/v) PEG 3350