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
2.6.99.2
-
RECOMMENDED NAME
GeneOntology No.
pyridoxine 5'-phosphate synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
reaction mechanism
-
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
reaction mechanism, the enzyme shows phosphomutase activity
-
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
-
-
-
-
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
reaction energetics and mechanism, active site structure, substrate binding structure, determination of conformation states of the enzyme during reaction from apo to single occupied transitional binding state and to fully occupied state
-
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
reaction mechanism, active site structure, substrate and product binding structures, structure-function relationship
-
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
reaction mechanism, active site structure, substrate binding structure, structure-function relationship
-
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
show the reaction diagram
reaction mechanism, Arg20 is involved in substrate binding, active site structure, structure-function relationship
-
PATHWAY
KEGG Link
MetaCyc Link
Metabolic pathways
-
pyridoxal 5'-phosphate biosynthesis I
-
Vitamin B6 metabolism
-
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
230310-47-1
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
P0A794
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
-
i.e. PNP
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
involved in the de novo synthesis of vitamin B6
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
key enzyme in the group of pdx gene-encoded enzymes involved in the de novo synthesis of vitamin B6
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
last step in the pyridoxine 5'-phosphate biosynthetic pathway, overview
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
the enzyme is involved in biosynthesis of vitamin B6
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
1-deoxy-D-xylose 5-phosphate binding structure
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
P0A794
1-deoxy-D-xylulose 5-phosphate binding structure
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
Arg20 is involved in substrate binding
product binding structure
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
multistep ring closure reaction, the phosphate group of the substrate is required for activity
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
the enzyme shows phosphomutase activity transfering the 5-phosphoryl group of 1-deoxy-D-xylose 5-phosphate to the 4-hydroxyl at some point in the reaction, the phosphate group of the substrate is required for activity, reaction mechanism, overview
i.e. pyridoxol phosphate
-
?
additional information
?
-
-
no activity with 1-deoxy-D-xylose
-
-
-
additional information
?
-
-
1-deoxy-D-xylulose is no substrate
-
-
-
additional information
?
-
-
free alcohol deoxyxylulose is no substrate
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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
P0A794
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
involved in the de novo synthesis of vitamin B6
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
key enzyme in the group of pdx gene-encoded enzymes involved in the de novo synthesis of vitamin B6
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
last step in the pyridoxine 5'-phosphate biosynthetic pathway, overview
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
show the reaction diagram
-
the enzyme is involved in biosynthesis of vitamin B6
-
-
?
additional information
?
-
-
no activity with 1-deoxy-D-xylose
-
-
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
additional information
-
thermodynamics
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
-
assay at
7.8
-
-
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-
assay at
PDB
SCOP
CATH
ORGANISM
Burkholderia pseudomallei (strain 1710b)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain 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)
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
octamer
-
in solution, crystal structure
dimer
-
the enzyme contains one abundant TIM barrel fold domain, intersubunit contacts are mediated by 3 additional helices, respective to the classical TIM barrel helices
additional information
-
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 ACCESSION NO.
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
-
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
-
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
-
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
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
recombinant enzyme by hydroxylapatite and ion exchange chromatography, and gel filtration
-
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pharmacology
-
the enzyme is a target for drug development in the treatment of human pathogens being capable, in contrast to the hosts, to synthesize pyridoxine 5'-phosphate