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4.3.3.6: pyridoxal 5'-phosphate synthase (glutamine hydrolysing)

This is an abbreviated version!
For detailed information about pyridoxal 5'-phosphate synthase (glutamine hydrolysing), go to the full flat file.

Word Map on EC 4.3.3.6

Reaction

D-ribose 5-phosphate
+
D-glyceraldehyde 3-phosphate
 +
L-glutamine
=
pyridoxal 5'-phosphate
 +
L-glutamate
 + 3 H2O +
phosphate

Synonyms

Pdx1, PDX2, PdxS, Ph1355, PLP synthase, PLP-synthase complex, PLPS, pyridoxal 5'-phosphate synthase, pyridoxal 5-phosphate synthase, pyridoxal 5-phosphate synthase Snz1, pyridoxal biosynthesis lyase, pyridoxal biosynthesis lyase PdxS, Rv2606c, Snz1

ECTree

     4 Lyases
         4.3 Carbon-nitrogen lyases
             4.3.3 Amine-lyases
                4.3.3.6 pyridoxal 5'-phosphate synthase (glutamine hydrolysing)

Crystallization

Crystallization on EC 4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolysing)

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor diffusion, 3D structure of the pyridoxal 5'-phosphate synthase complex with substrate glutamine bound as well as those of the individual synthase and glutaminase subunits Pdx1 and Pdx2, respectively. The complex is made up of 24 protein units assembled like a cogwheel, a dodecameric Pdx1 to which 12 Pdx2 subunits attach. Macromolecular assembly is directed by an N-terminalalpha-helix on the synthase. Interaction with the synthase subunit leads to glutaminase activation, resulting in formation of an oxyanion hole, a prerequisite for catalysis
sitting drop vapor diffusion, to investigate the mechanism of the synthase subunit, crystal structures are obtained for three intermediate states of the Geobacillus stearothermophilus intact PLPS or its synthase subunit. The structures capture the synthase active site at three distinct steps in its complicated catalytic cycle, provide insights into the elusive mechanism, and illustrate the coordinated motions within the synthase subunit that separate the catalytic states
purified recombinant enzyme, hanging drop vapour diffusion method, mixing of 00.0015 ml of 22 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 5 mM 2-mercaptoethanol, with 0.0015 ml of reservoir solution, containing 8% PEG 8000, 0.1 M 3-[cyclohexylamino]-1-propanesulfonic acid, pH 10.5, and 0.2 M sodium chloride, and equilibration against 0.5 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement using the Thermotoga maritima PdxS, PDB code 2ISS
Pdx1, chimeric complex of Pdx1 and Pdx2 from Plasmodium falciparum
chimeric complex of Pdx2 and Pdx1 from Plasmodium berghei
-
2-methyl-2,4-pentanediol
crystallization at 22°C using 2-methyl-2,4-pentanediol as a precipitant. Crystals of PdxS diffract to 2.61 A resolution and belong to the monoclinic space group P2(1), with unit-cell parameters a = 59.30, b = 178.56, c = 109.23 A, beta = 102.97°. The asymmetric unit contained six monomers
crystallized at 23°C using 2-methyl-2,4-pentanediol as a precipitant. Crystals of apo and ribose 5'-phosphate complex forms of PdxS diffract to 2.7 A and 3.1 A resolution, respectively, and belong to the monoclinic space group P2(1)
hanging-drop vapour-diffusion method, 296 K, 2-methyl-2,4-pentanediol
hanging-drop vapour diffusion method, 16°C