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Information on EC 4.1.99.12 - 3,4-dihydroxy-2-butanone-4-phosphate synthase and Organism(s) Escherichia coli and UniProt Accession P0A7J0
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4.1.99.12 3,4-dihydroxy-2-butanone-4-phosphate synthaseIUBMB Comments
Requires a divalent cation, preferably Mg2+, for activity . The reaction involves an intramolecular skeletal rearrangement, with the bonds in D-ribulose 5-phosphate that connect C-3 and C-5 to C-4 being broken, C-4 being removed as formate and reconnection of C-3 and C-5 . The phosphorylated four-carbon product (L-3,4-dihydroxybutan-2-one 4-phosphate) is an intermediate in the biosynthesis of riboflavin .
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- 4.1.99.12
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disinfection
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trihalomethanes
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haloacetic
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brominate
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halogen
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haloacetonitriles
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chloramination
- bromide
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genotoxicity
- chloroform
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effluent
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wastewater
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iodin
- ozone
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swimming
-
humic
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unregulated
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trichloronitromethane
- n-nitrosodimethylamine
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carbonaceous
- chloral
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speciation
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dichloroacetic
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dichloroacetonitrile
- monochloramine
- haloketones
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bromodichloromethane
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swimmers
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fulvic
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hypochlorite
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non-regulated
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micropollutants
- clo2
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pilot-scale
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n-nitrosamines
- naclo
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excitation-emission
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bromoacetic
- chlorite
-
ballast
-
shower
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acid-like
- pipe
-
potable
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suwannee
- drug development
- synthesis
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nanofiltration
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biofiltration
- bromoform
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indoor
- iodate
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
dbps, dhbps, 3,4-dihydroxy-2-butanone-4-phosphate synthase, mtb-dhbps, mtb-riba2, atriba1, dhbp synthase, dihydroxybutanone phosphate synthase, atriba2, vdhbps, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3,4-dihydroxy-2-butanone 4-phosphate synthase
DHBP synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
reaction mechanism
-
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
catalytic mechanism
-
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
catalytic reaction mechanism, substrate recognition and active site structure, active site consists of three glutamates, two aspartates, two histidines, and a cysteine which may provide the means for general acid and base catalysis and for coordinating the Mg2+ cofactor within the active site
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
D-ribulose 5-phosphate formate-lyase (L-3,4-dihydroxybutan-2-one 4-phosphate-forming)
Requires a divalent cation, preferably Mg2+, for activity [1]. The reaction involves an intramolecular skeletal rearrangement, with the bonds in D-ribulose 5-phosphate that connect C-3 and C-5 to C-4 being broken, C-4 being removed as formate and reconnection of C-3 and C-5 [1]. The phosphorylated four-carbon product (L-3,4-dihydroxybutan-2-one 4-phosphate) is an intermediate in the biosynthesis of riboflavin [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
D-ribulose 5-phosphate
formate + L-3,4-dihydroxybutan-2-one 4-phosphate
-
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
-
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
-
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
step in biosynthesis of vitamin B2, riboflavin
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
the enzyme is important in riboflavin biosynthesis, overview
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
the enzyme is involved in the pathway of riboflavin biosynthesis
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
the enzyme is involved in the pathway of riboflavin biosynthesis
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
the enzyme is involved in the pathway of riboflavin biosynthesis, overview
-
-
?
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
D-ribulose 5-phosphate
formate + L-3,4-dihydroxybutan-2-one 4-phosphate
-
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
step in biosynthesis of vitamin B2, riboflavin
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
the enzyme is important in riboflavin biosynthesis, overview
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
the enzyme is involved in the pathway of riboflavin biosynthesis
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
the enzyme is involved in the pathway of riboflavin biosynthesis
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
the enzyme is involved in the pathway of riboflavin biosynthesis, overview
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
development of a spectrophotometric/colorimetric assay method, overview
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
-
the enzyme is involved in riboflavin biosynthesis. Up-regulation of DHBP synthase is evidenced as one of the first line strategies to cope with imbalance of energy production and vital adaptation
physiological function
3,4-dihydroxy-2-butanone 4-phosphate (DHBP) and GTP are the precursors for riboflavin biosynthesis
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
23000
-
2 * 23000, SDS-PAGE, hydrodynamic analysis, NMR structure study, 2 * 23351, mass spectrometry
23351
-
2 * 23000, SDS-PAGE, hydrodynamic analysis, NMR structure study, 2 * 23351, mass spectrometry
46300
-
recombinant enzyme, hydrodynamic analysis, NMR structure study, analytical ultracentrifugation at 4°C, overview
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
dimer
-
2 * 23000, SDS-PAGE, hydrodynamic analysis, NMR structure study, 2 * 23351, mass spectrometry
dimer
three-dimensional structure, structure-activity relationship study using NMR spectroscopy, residue-specific isotope labeling, and protein deuteration strategies, solution structure, overview
additional information
-
hydrodynamic analysis, NMR structure study, isotope labeling, the homodimeric protein obeys strict C2 symmetry, overview
additional information
structure determination and analysis of functions of single residues, overview, dimer interface structure, localization of the active site, sequence and structure comparison
additional information
-
structure determination and analysis of functions of single residues, overview, dimer interface structure, localization of the active site, sequence and structure comparison
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, hanging drop vapour diffusion method at room temperature, 4-5 days, 0.0022 ml of protein solution containing 24 mg/ml protein in 50 mM Tris-HCl pH 7.5, is mixed with 0.0007 ml of precipitating well solution containing 3 M CsCl, 3 M Cs-formate, 20 mM Bis-Tris-propane-NaOH, pH 6.9, or 6 M sodium formate, 25 mM HEPES-NaOH, pH 7.0, labeling with 1.5 mM Au(CN)2, X-ray diffraction structure determination and analysis at 1.4-2.4 A resolution, multiwavelength anomalous diffraction
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
engineering of Escherichia coli for increased riboflavin production: overexpression of gene ribB to increase the flux from ribulose 5-phosphate to 3,4-dihydroxybutan-2-one 4-phosphate. Then ndk and gmk genes are overexpressed to enhance GTP supply. Subsequently, a R419L mutation is introduced into purA to reduce the flux from IMP to AMP. Co-overexpression of mutant purF and prs genes further increased riboflavin production. The final strain RF18S produces 387.6 mg riboflavin per liter with a yield of 44.8 mg riboflavin per gram glucose in shake-flask fermentations. The final titer and yield are 72.2% and 55.6%. Mutant strain and method evaluation, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from strain Bl21(DE3) by hydrophobic interaction and anion exchange chromatography, and ultrafiltration
-
recombinant enzyme from strain M15 by anion exchange chromatography and gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
increase of 3,4-dihydroxy-2-butanone 4-phosphate synthase upon exposure to Cd2+
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
drug development
-
the enzyme is a target in antimicrobial inhibitor development, structure-based inhibitor design
drug development
the enzyme is an attractive target for antibiotics, design of mechanism-based inhibitors
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Picollelli, M.A.; Viitanen, P.V.; Jordan, D.B.
Spectrophotometric determination of 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
Anal. Biochem.
287
347-349
2000
Escherichia coli, Escherichia coli W3110 / ATCC 27325
Richter, G.; Kelly, M.; Krieger, C.; Yu, Y.; Bermel, W.; Karlsson, G.; Bacher, A.; Oschkinat, H.
NMR studies on the 46-kDa dimeric protein, 3,4-dihydroxy-2-butanone 4-phosphate synthase, using 2H, 13C, and 15N-labelling
Eur. J. Biochem.
261
57-65
1999
Escherichia coli
Goetze, E.; Kis, K.; Eisenreich, W.; Yamauchi, N.; Kakinuma, K.; Bacher, A.
Biosynthesis of riboflavin. Stereochemistry of the 3,4-dihydroxy-2-butanone 4-phosphate synthase reaction
J. Org. Chem.
63
6456-6457
1998
Escherichia coli
-
Kelly, M.J.; Ball, L.J.; Krieger, C.; Yu, Y.; Fischer, M.; Schiffmann, S.; Schmieder, P.; Kuhne, R.; Bermel, W.; Bacher, A.; Richter, G.; Oschkinat, H.
The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site
Proc. Natl. Acad. Sci. USA
98
13025-13030
2001
Methanocaldococcus jannaschii, Escherichia coli (P0A7J0), Escherichia coli
Liao, D.I.; Calabrese, J.C.; Wawrzak, Z.; Viitanen, P.V.; Jordan, D.B.
Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis
Structure
9
11-18
2001
Escherichia coli (P0A7J0), Escherichia coli
Isarankura-Na-Ayudhya, P.; Isarankura-Na-Ayudhya, C.; Treeratanapaiboon, L.; Kasikun, K.; Thipkeaw, K.; Prachayasittikul, V.
Proteomic profiling of Escherichia coli in response to heavy metals stress
Eur. J. Sci. Res.
25
679-688
2009
Escherichia coli, Escherichia coli TG1
-
Xu, Z.; Lin, Z.; Wang, Z.; Chen, T.
Improvement of the riboflavin production by engineering the precursor biosynthesis pathways in Escherichia coli
Chin. J. Chem. Engin.
23
1834-1839
2015
Escherichia coli (P0A7J0), Escherichia coli K-12 / MG1655 (P0A7J0)
-
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