Information on EC 2.6.99.2 - pyridoxine 5'-phosphate synthase

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The enzyme appears in viruses and cellular organisms

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
pyridoxal 5'-phosphate biosynthesis I
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vitamin B6 metabolism
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Vitamin B6 metabolism
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Metabolic pathways
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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
UNIPROT
ORGANISM
Q3JQ80
Burkholderia pseudomallei (strain 1710b);
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168);
Escherichia coli (strain K12);
Q02HS5
Pseudomonas aeruginosa (strain UCBPP-PA14);
Q8ZCP4
Yersinia pestis;
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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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pharmacology
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