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2.5.1.55: 3-deoxy-8-phosphooctulonate synthase

This is an abbreviated version!
For detailed information about 3-deoxy-8-phosphooctulonate synthase, go to the full flat file.

Word Map on EC 2.5.1.55

Reaction

phosphoenolpyruvate
+
D-arabinose 5-phosphate
 +
H2O
=
3-deoxy-D-manno-octulosonate 8-phosphate
 +
phosphate

Synonyms

2-dehydro-3-deoxy-D-octonate-8-phosphate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating), 2-dehydro-3-deoxyphosphooctonate aldolase, 2-keto-3-deoxy-8-phosphooctonic acid synthetase, 2-keto-3-deoxy-8-phosphooctonic synthetase, 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase, 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase, 3-deoxy-D-manno-2-octulosonic acid-8-phosphate synthase, 3-deoxy-D-manno-octulosonate 8-phosphate synthase, 3-deoxy-D-manno-octulosonate 8-phosphate synthetase, 3-deoxy-D-manno-octulosonate-8-phosphate synthase, 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase, 3-deoxy-D-mannooctulosonate-8-phosphate synthetase, 3-deoxyoctulosonic 8-phosphate synthetase, 3-eoxy-D-manno-octulosonate 8-phosphate synthase, 8-phospho-2-dehydro-3-deoxy-D-octonate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating), aldolase, phospho-2-keto-3-deoxyoctonate, AtkdsA1, AtkdsA2, EC 4.1.2.16, HpKDO8PS, KDO 8-phosphate synthetase, KDO-8-P synthase, KDO-8-P synthetase, Kdo-8-phosphate synthase, KDO8-P, Kdo8P synthase, KDO8PS, KDOPS, KDPO synthetase, KdsA, KdsA1, KdsA2, metal-independent 3-deoxy-D-manno-octulosonate 8-phosphate synthase, metal-independent KDO8PS, NmeKDO8PS, Phospho-2-dehydro-3-deoxyoctonate aldolase, phospho-2-keto-3-deoxyoctonate aldolase

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)
                2.5.1.55 3-deoxy-8-phosphooctulonate synthase

Crystallization

Crystallization on EC 2.5.1.55 - 3-deoxy-8-phosphooctulonate synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
data reading at -173°C
structure of the metal-free and Cd2+ forms of the enzyme are determined in the uncomplexed state and in complex with various combinations of phosphoenolpyruvate, arabinose 5-phosphate and erythrose 4-phosphate
-
X-ray structure of wild-type enzyme shows that when both phosphoenolpyruvate and D-arabinose 5-phosphate bind, the active site becomes isolated from the environment due to a conformational change of the L7 loop. The structures of the R106G mutant, without substrates, and with phosphoenolpyruvate and phosphoenolpyruvate plus D-arabinose 5-phosphate bound reveal that in R106G closure of the L7 loop is impaired
purified recombinant enzyme, hanging-drop vapor diffusion method, mixing of 300 nl of 10 mg/ml protein in 30 mM Tris-HCl, pH 8.0, 200 mM NaCl with 300 nl reservoir solution containing 28% v/v PEG 400, 0.1 M HEPES, pH 7.5, and 0.2 M CaCl2, X-ray diffraction structure determinatin and analysis
crystallization is performed by vapor diffusion in hanging drops
crystals are grown at 23°C by vapor diffusion in hanging drops, crystal structures of the enzyme in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor
structures of apo-enzyme and of binary complexes with the substrates phosphoenolpyruvate, the product 2-dehydro-3-deoxy-D-octonate 8-phosphate and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate
purified recombinant His-tagged wild-type and mutant H204A enzymes in apoform, or wild-type enzyme complexed with Zn2+ or Cd2+, hanging drop vapor diffusion method, mixing of 0.001 ml of protein solution, containing inhibitor in a 1:2 ratio, with 0.001 ml of reservoir solution, containing 18% PEG 3350, 0.1 M HEPES, pH 7.5, and 0.25 M magnesium chloride hexahydrate, equilibration against reservoir solution, 20°C, 14 days, X-ray diffraction structure determination and analysis at 2.0 A resolution, molecular replacement and modelling
purified recombinant mutant enzymes, hanging-drop vapor diffusion, mixing of 0.002 ml of protein solution containing 20 mg/ml protein in 10 mM BTP, pH 7.5, with 0.002 ml of reservoir solution containing 100 mM sodium acetate, pH 4.6, and 0.6-3.0 M NaCl, equilibration against 0.5 ml reservoir solution, 20°C, 24 h, X-ray diffraction structure determination and analysis at 1.75-2.10 A resolution
-
the X-ray structures, determined for the mutants with altered KANRS motif, indicate no gross structural penalty resulting from mutation, but the subtle changes observed in the active sites of these mutant proteins correlate with their altered catalytic function
-
vapor-diffusion hanging drop method, pH 4.6 and pH 5.0, no diffraction quality crystals at higher pH in the range of the active enzyme
homology modeling based on the crystal structure of the KDO8P synthase from Escherichia coli, PDB entry 1X6U
purified recombinant His6-tagged enzyme, sitting drop vapour diffusion method, mixing of 0.003 ml of 5 mg/ml protein in 0.2 M Tris-HCl, pH 7.4, 0.1 M NaCl, 0.05% 2-mercaptoethanol, and 0.1 mM phosphoenolpyruvate with 0.0015 ml of reservoir solution containing 0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, 18% w/v PEG 8000, 20°C, 2 days, X-ray diffraction structure determination and analysis at 2.8 A resolution, molecular replacementusing structure PDB ID 1g7v and model building
-