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Information on EC 2.6.99.2 - pyridoxine 5'-phosphate synthase and Organism(s) Escherichia coli and UniProt Accession P0A794
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2.6.99.2 pyridoxine 5'-phosphate synthaseIUBMB Comments
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 .
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Reaction Schemes
Synonyms
pnp synthase, pyridoxine 5'-phosphate synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
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
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
reaction mechanism, Arg20 is involved in substrate binding, active site structure, structure-function relationship
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
reaction mechanism
-
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O
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
reaction mechanism, the enzyme shows phosphomutase activity
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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
230310-47-1
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
1-deoxy-D-xylose 5-phosphate binding structure
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
1-deoxy-D-xylulose 5-phosphate binding structure
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
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
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
-
-
i.e. PNP
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
-
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
-
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
-
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
-
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
-
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
?
-
-
free alcohol deoxyxylulose is no substrate
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
-
-
-
-
?
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
pyridoxine 5'-phosphate + phosphate + H2O
-
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
-
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
-
the enzyme is involved in biosynthesis of vitamin B6
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
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
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
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
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme by hydroxylapatite and ion exchange chromatography, and gel filtration
APPLICATION
ORGANISM
UNIPROT
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Laber, B.; Maurer, W.; Scharf, S.; Stepusin, K.; Schmidt, F.S.
Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein
FEBS Lett.
449
45-48
1999
Escherichia coli
Cane, D.E.; Du, S.; Robinson, J.K.; Hsiung, Y.; Spenser, I.D.
Biosynthesis of vitamin B6: enzymatic conversion of 1-deoxy-D-xylulose-5-phosphate to pyridoxol phosphate
J. Am. Chem. Soc.
121
7722-7723
1999
Escherichia coli
-
Garrido Franco, M.; Huber, R.; Schmidt, F.S.; Laber, B.; Clausen, T.
Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme
Acta Crystallogr. Sect. D
56
1045-1048
2000
Escherichia coli
Yeh, J.I.; Du, S.; Pohl, E.; Cane, D.E.
Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate
Biochemistry
41
11649-11657
2002
Escherichia coli (P0A794)
Garrido-Franco, M.
Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond
Biochim. Biophys. Acta
1647
92-97
2003
Escherichia coli, Neisseria gonorrhoeae, Neisseria meningitidis, Yersinia pestis, Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Typhi, Vibrio cholerae serotype O1
Garrido-Franco, M.; Laber, B.; Huber, R.; Clausen, T.
Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis
J. Mol. Biol.
321
601-612
2002
Escherichia coli (P0A794)
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