Information on EC 2.6.99.2 - pyridoxine 5'-phosphate synthase

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The expected taxonomic range for this enzyme is: Proteobacteria

EC NUMBER
COMMENTARY hide
2.6.99.2
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RECOMMENDED NAME
GeneOntology No.
pyridoxine 5'-phosphate synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Metabolic pathways
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pyridoxal 5'-phosphate biosynthesis I
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vitamin B6 metabolism
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Vitamin B6 metabolism
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SYSTEMATIC NAME
IUBMB Comments
1-deoxy-D-xylulose-5-phosphate:3-amino-2-oxopropyl phosphate 3-amino-2-oxopropyltransferase (phosphate-hydrolysing; cyclizing)
In Escherichia coli, the coenzyme pyridoxal 5'-phosphate is synthesized de novo by a pathway that involves EC 1.2.1.72 (erythrose-4-phosphate dehydrogenase), EC 1.1.1.290 (4-phosphoerythronate dehydrogenase), EC 2.6.1.52 (phosphoserine transaminase), EC 1.1.1.262 (4-hydroxythreonine-4-phosphate dehydrogenase), EC 2.6.99.2 (pyridoxine 5'-phosphate synthase) and EC 1.4.3.5 (with pyridoxine 5'-phosphate as substrate). 1-Deoxy-D-xylulose cannot replace 1-deoxy-D-xylulose 5-phosphate as a substrate [3].
CAS REGISTRY NUMBER
COMMENTARY hide
230310-47-1
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
additional information
?
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no activity with 1-deoxy-D-xylose
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
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thermodynamics
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
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assay at
7.8
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia pseudomallei (strain 1710b)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Pseudomonas aeruginosa (strain UCBPP-PA14)
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
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the enzyme contains one abundant TIM barrel fold domain, intersubunit contacts are mediated by 3 additional helices, respective to the classical TIM barrel helices
octamer
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in solution, crystal structure
additional information
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enzyme structure, the monomer comprises a single domain which folds as a (beta/alpha)8 barrel or TIM barrel, 3 extra helices complete the scaffold mediating the intersubunit contact
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
12 mg/ml purified recombinant enzyme, wild-type or selenomethionine-labeled, in 10 mM Tris-HCl, pH 7.5, 0.4 mM potassium phosphate, 1.21 mM NaCl, 8% PEG 8000, 9% PEG 1000, 10% glycerol, and 4 mM 1-deoxy-D-xylulose, hanging drop vapour diffusion method, X-ray diffraction structure determination and analysis at 1.96-3.2 A resolution
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6 mg/ml purified recombinant enzyme in 2 mM Tris-HCl, pH 8.0, 0.003 ml mixed with 0.0015 ml precipitation solution, equilibration against 0.5 ml reservoir solution, sitting drop vapour diffusion method, method 1: 0.1 M sodium acetate, pH 4.6, 8% PEG 4000 as precipitant and 0.1 M L-cysteine as additive, triangular-shaped crystals within 10 days, method 2: precipitant solution contains 10% PEG 6000, 2 M NaCl, slow crystal growth, 6 weeks, microseeding into protein solution of 13.5 mg/ml protein, 2 mM Tris-HCl, pH 8.8, 1 day, or hanging drop vapour diffusion method over 1 week, method evaluation, X-ray diffraction and preliminary structure determination and analysis at 2.6 A resolution
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purified enzyme in complex with products pyridoxine 5'-phosphate and phosphate, the enzyme crystals are incubated with 5 mM product solution for 1 h, X-ray diffraction structure determination and analysis at 2.3 A resolution
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purified enzyme, the native enzyme crystals are incubated with 2.5 mM glyceraldehyde 3-phosphate and 2.5 mM 1-deoxy-D-xylulose 5-phosphate for 3 hours, in 10 mM or 100 mM phosphate for 3 days, and for another 3 days in 20 mM 1-deoxy-D-xylulose 5-phosphate, X-ray diffraction structure determination and analysis at 2.3 A resolution
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme by hydroxylapatite and ion exchange chromatography, and gel filtration
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pharmacology
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