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2.5.1.54: 3-deoxy-7-phosphoheptulonate synthase

This is an abbreviated version!
For detailed information about 3-deoxy-7-phosphoheptulonate synthase, go to the full flat file.

Word Map on EC 2.5.1.54

Reaction

phosphoenolpyruvate
+
D-erythrose 4-phosphate
 +
H2O
=
3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate
 +
phosphate

Synonyms

2-dehydro-3-deoxy-D-arabino-heptonate-7-phosphate D-erythrose-4-phosphate-lyase (pyruvate-phosphorylating), 2-dehydro-3-deoxy-phosphoheptanoate aldolase, 2-dehydro-3-deoxy-phosphoheptonate aldolase, 2-keto-3-deoxy-D-arabino-heptonic acid 7-phosphate synthetase, 3-deoxy-7-phosphoheptulonate synthase, 3-deoxy-D-arabino heptulosonate 7-phosphate synthase, 3-deoxy-D-arabino-2-heptulosonic acid 7-phosphate synthetase, 3-deoxy-D-arabino-heptolosonate-7-phosphate synthetase, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase, 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, 3-deoxy-D-arabino-heptulosonic acid 7-phosphate synthase, 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase, 3-deoxy-D-arabinoheptulosonate-7-phosphate synthetase, 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate D-erythrose-4-phosphate-lyase (pyruvate-phosphorylating), 7-phospho-2-keto-3-deoxy-D-arabino-heptonate D-erythrose-4-phosphate lyase (pyruvate-phosphorylating), aldolase, phospho-2-keto-3-deoxyheptanoate, Aro1A, Aro4, Aro4p, AroA, AroA(Q), aroF, AroFFR, AroG, D-erythrose-4-phosphate-lyase, D-erythrose-4-phosphate-lyase (pyruvate-phosphorylating), DAH7-P synthase, DAH7-P synthase (phe), DAH7P, DAH7P synthase, DAH7PS, DAHP synthase, DAHP synthase-phe, DAHP synthase-trp, DAHP synthase-tyr, DAHP(Phe), DAHPS, DAHPS(Tyr), Dax1, deoxy-D-arabino-heptulosonate-7-phosphate synthetase, DHS, DHS1, DS-Co, DS-Mn, EC 4.1.2.15, KDPH synthase, KDPH synthetase, More, mtDAH7Ps, MtDS, NCgl0950 DAHP synthase, NCgl2098 DAHP synthase, Nme-DAH7PS, OsDAHPS, PF1690, phospho-2-dehydro-3-deoxyheptonate aldolase, phospho-2-keto-3-deoxyheptanoate aldolase, Phospho-2-keto-3-deoxyheptonate aldolase, phospho-2-keto-3-deoxyheptonic aldolase, phospho-2-oxo-3-deoxyheptonate aldolase, phzC, TmaDAH7PS

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)
                2.5.1.54 3-deoxy-7-phosphoheptulonate synthase

Crystallization

Crystallization on EC 2.5.1.54 - 3-deoxy-7-phosphoheptulonate synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with a manganese ion and phosphoenolpyruvate. Crystals contain a tetramer in the asymmetric unit. A water molecule occupies the presumed binding site for the phosphate group of 4-erythrose 4-phosphate
modeling of the three dimensional structure of the type II enzyme present in Arabidopsis thaliana and comparison with type I DAHPS. The enzyme belongs to the (beta/alpha)8 TIM barrel family. At the N-terminus of the Arabidopsis thaliana enzyme, there are three non-core helices, alpha0a (Ala72-Lys83), alpha0b (Ala94-Ala106) and alpha0c (Ala113-Val128), but no beta0, in contrast to the microbial type II DAHPS. Also, the (I/L)GAR motif in the type I DAHPS is substituted with xGxR in the case of type II DAHPS. A motif NK(/I)PGR(/K) is present in the sequences of type II DAHPS including At-DAHPS
structure of N-terminal domain AroQ in complex with citrate and chlorogenic acid at 1.9 A and 1.8 A resolution, respectively. Helix H2' undergoes uncoiling at the first turn and increases the mobility of loop L1'. The side chains of Arg45, Phe46, Arg52 and Lys76 undergo conformational changes, which may play an important role in DAHPS regulation by the formation of the domain-domain interface. Chlorogenic acid binds with a higher affinity than chorismate
in complex with inhibitor 3-deoxy-D-arabinoheptulosonate-7-phosphate oxime
native and selenomethionine-substituted protein, in complex with phosphoenolpyruvate and Mn2+, mutant E24Q in complex with phosphoenolpyruvate and Mn2+
Phe-sensitive isozyme, enzyme-Mn2+-2-phosphoglycolate-complexes, hanging drop vapour diffusion method, room temperature, all solutions, except the MnSO4 and the enzyme solution, are treated with Chelex-100 to remove metals, 0.2 mM enzyme subunit solution: 0.37 MnSO4, 4.2 mM 2-phosphoglycolate, 0.1 M Li2SO4, 12% PEG 100 w/v, 20% ethanol v/v, 50 mM 1,3-bis[tris(hydroxy-methyl)methylamino]propane buffer, pH 8.7, reservoir solution: 19% PEG 1000, 0.1 M Li2SO4, 20% ethanol v/v, 50 mM 1,3-bis[tris(hydroxy-methyl)methylamino]propane buffer, X-ray diffraction structure determination and analysis
Phe-sensitive isozyme, hanging drop vapour diffusion method, 22°C, with or without inhibitor phenylalanine, at pH 6.3-9.4, 0.1-0.2 M monovalent cations, PEG 1000-4000, 0.01 ml protein solution + 0.3 ml precipitant solution, X-ray diffraction structure determination and analysis
-
structures of apo form and complex with the inhibitor tyrosine at 2.5 and 2.0 A resolutions, respectively. DAHPS(Tyr) has a typical (beta/alpha)8 TIM barrel, which is decorated with an N-terminal extension and an antiparallel beta sheet. Inhibitor tyrosine binds at a cavity formed by residues of helices alpha3, alpha4, strands beta6a, beta6b and the adjacent loops, and directly interacts with residues P148, Q152, S181, I213 and N8*. Conformational changes of residues P148, Q152 and I213 initiate a transmission pathway to propagate the allosteric signal from the tyrosine-binding site to the active site
structures in complex with Mn2+ and Mn+ and phosphoenolpyruvate, to 1.95 A resolution. The domains assemble as a tetramer, from either side of which chorismate mutase-like regulatory domains asymmetrically emerge to form a pair of dimers. Domain organization suggests that chorismate/prephenate binding promotes a stable interaction between the discrete regulatory and catalytic domains and supports a mechanism of allosteric inhibition similar to tyrosine/phenylalanine control of a related DAHPS class. The catalytic domain adopts a classic TIM barrel (alpha/beta)8 fold. The active site is located on the inside of the C-terminal end of the barrel and is formed by several alpha-beta-connecting loops and two beta-strands. In the holo structure, a manganese ion is present at the active site. In the phosphoenolpyruvate structure, the substrate is adjacent to the manganese ion in a similar position as has been observed in related enzymes
-
in complex with chorismate mutase, hanging-drop method, in 20 mM BTP, pH 7.5, 150 mM NaCl, 0.5 mM tris(2-carboxyethyl)phosphine hydrochloride, 0.2 mM phosphoenolpyruvate and 0.1 mM MnCl2, crystallization after 2 months with no ammonium sulfate and 0.1 M Tris-HCl, pH 7.9-8.0 and PEG 400 or glycerol
in complex with chorismate mutase, streak-seeding conditions in 20 mM BTP (1,3-bis[tris(hydroxymethyl)methylamino]propane), pH 7.5, 150 mM NaCl, 0.5 mM TCEP [tris(2-carboxyethyl)phosphine hydrochloride], 0.2 mM phosphoenolpyruvate, crystallization by 0.9 M ammonium sulfate, 100 mM Tris, pH 7.9 to 8.0, and 1 to 5% PEG 400
recombinant protein, after coexpression with Escherichia coli chaperonins GroEL and GroES in Escherichia coli, crystallized as native and selenomethionine-substituted proten
-
purified enzyme mutant S213G with phosphoenolpyruvate and Mn2+, hanging drop vapor diffusion, mixing of 0.001 ml of 11 mg/mL in 10 mM BTP buffer, pH 7.3, in a 1:1 v/v with a reservoir solution containing 0.2 M trimethylamine N-oxide, 0.1 M Tris, pH 8.5, 15-20% w/v PEG 2000 MME, 0.4 mM MnSO4, and 0.4 mM phosphoenolpyruvate, equilibration against 0.5 ml of reservoir solution, 20°C, 3 days, X-ray diffractin structure determination and analysis at 2.0-2.1 A resolution
purified recombinant enzyme complexed with inhibitors (S)-phospholactate, (R)-phospholactate, and vinyl phosphonate, hanging drop vapour diffusion method, mixing of 0.001 ml of 10 mg/mL protein in 10 mM bis(tris(hydroxymethyl)methylamino)propane, pH 7.3, and 5 mM inhibitor, with 0.001 ml of crystallisation buffer containing 0.1 Tris HCl, pH 7.3, 0.2 M trimethyl-amino-N-oxide, 0.4 mM MnSO4, and 15-20% w/v PEG 2000MME, equilibration over 0.5 ml of reservoir solution, 20°C, 3 days, X-ray diffraction structure determination and analysis at 1.76-2.34 A resolution
purified recombinant enzyme mutant R126S, hanging drop vapour diffusion method, mixing of 0.001 ml of 10 mg/mL protein solution with 0.001 ml of crystallisation buffer containing 0.1 Tris HCl, pH 7.3, 0.2 M trimethyl-amino-N-oxide, 0.6 mM MnSO4, and 15-20% w/v PEG 2000MME, equilibration over 0.5 ml of reservoir solution, 20°C, 7 days, X-ray diffraction structure determination and analysis at 2.0 A resolution
structure of type II DAH7PS, encoded by phzC as part of the duplicated phenazine biosynthetic cluster, to 2.7 A resolution, space group C2221 with two DAH7PS chains present in the asymmetric unit
hanging-drop vapor diffusion, ctystal structure of wild-type enzyme and mutant enzyme I181D
recombinant enzyme, in complex with phosphoenolpyruvate
Tyr-sensitive isozyme, hanging drop vapour diffusion method, protein solution in 1:1 mixture with precipitant, 0.004 ml, + 1 ml precipitant solution: 1. 50 mM KH2PO4, 20% polyethylene glycol 8000 w/v or 2. 0.1 M Tris, pH 9.0, 10 mM NiCl2, 20% polyethylene glycol monomethylester 2000 w/v, room temperature for 3 days, X-ray diffraction structure analysis, usage of cryoprotectant glycerol for investigations
-
crystals grown in presence of phosphoenolpyruvate and Cd2+, soaked with erythrose 4-phosphate
-
molecular modeling of structure. The monomeric structure of Aro1A is a (beta/alpha)8 barrel structure. Phosphoenolpyruvate combines with residues R60, Q116, S119, K141, and R171 through eight hydrogen bonds. D-erythrose 4-phosphate combines with residues R60, K65, Q116, S119, K141, and R171 through nine hydrogen bonds