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Information on EC 4.1.99.12 - 3,4-dihydroxy-2-butanone-4-phosphate synthase and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q60364
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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
-
trihalomethanes
-
haloacetic
-
brominate
-
halogen
-
haloacetonitriles
-
chloramination
- bromide
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genotoxicity
- chloroform
-
effluent
-
wastewater
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iodin
- ozone
-
swimming
-
humic
-
unregulated
-
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
-
fulvic
-
hypochlorite
-
non-regulated
-
micropollutants
- clo2
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pilot-scale
-
n-nitrosamines
- naclo
-
excitation-emission
-
bromoacetic
- chlorite
-
ballast
-
shower
-
acid-like
- pipe
-
potable
-
suwannee
- drug development
- synthesis
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nanofiltration
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biofiltration
- bromoform
-
indoor
- iodate
The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
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
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
active site and reaction mechanism, structure-function relationship, structural coordination spheres are important, residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity, Glu185 is essential for catalytic activity
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
active site architecture
-
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
reaction mechanism involving intramolecular skeletal rearrangement, a cluster of charged amino acid residues comprising Arg25, Glu26 and Glu28, Asp21 and Asp30 is essential for catalytic activity, as well as His164 and Glu185
-
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-dihydroxy-2-butanone-4-phosphate
step in the biosynthesis of riboflavin, vitamin B2, ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
a dimetal center is involved in substrate binding, structure-function relationship, overview
-
-
?
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
-
DHBPS supplies the building blocks for the assembly of the xylene ring of the vitamin B2, riboflavin, all eight C atoms of the xylene moiety are derived from the product of the enzyme
-
-
?
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
-
substrate binding structure involving a dimetal center, overview
the enzyme converts ribulose 5-phosphate into 3,4-dihydroxy-2-butanone 4-phosphate, while its C4 atom is released as formate
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
the reaction involves an intramolecular skeletal rearrangement, NMR study
-
-
?
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-dihydroxy-2-butanone-4-phosphate
step in the biosynthesis of riboflavin, vitamin B2, ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions
-
-
?
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
-
DHBPS supplies the building blocks for the assembly of the xylene ring of the vitamin B2, riboflavin, all eight C atoms of the xylene moiety are derived from the product of the enzyme
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
-
the enzyme is involved in the pathway of riboflavin biosynthesis
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
-
Ca2+ binding requires the binding of the substrate, binding involves Glu204, Glu97, and Asn207
Zn2+
-
bound at His164, binding involves His206, Glu132, and Glu128
additional information
additional information
the enzyme depends on divalent metal ions, a dimetal center is involved in substrate binding
additional information
-
substrate binding structure involving a dimetal center, overview
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25799
-
2 * 25799, recombinant enzyme, mass spectrometry and SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
structure-function relationship, overview
dimer
-
2 * 25799, recombinant enzyme, mass spectrometry and SDS-PAGE
dimer
-
three-dimensional structure, structure-activity relationship study using NMR spectroscopy, residue-specific isotope labeling, and protein deuteration strategies, solution structure, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme mutant H147S in complex with substrate ribulose 5-phosphate, monoclinic crystal form, X-ray diffraction structure determination and analysis at 1.55-1.7 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H147S
site-directed mutagenesis, the mutant enzyme shows about 10% of the wild-type enzyme activity
H147S
-
site-directed mutagenesis, the mutant shows about 10% of wild-type enzyme activity, crystal structure determination with bound substrate
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes from Escherichia coli by hydrophobic interaction and hydroxyapatite chromatography, and ultrafiltration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, expression of wild-type and mutant enzymes in Escherichia coli strains XL-1 Blue and M15
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Steinbacher, S.; Schiffmann, S.; Bacher, A.; Fischer, M.
Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate
Acta Crystallogr. Sect. D
60
1338-1340
2004
Methanocaldococcus jannaschii
Fischer, M.; Romisch, W.; Schiffmann, S.; Kelly, M.; Oschkinat, H.; Steinbacher, S.; Huber, R.; Eisenreich, W.; Richter, G.; Bacher, A.
Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii
J. Biol. Chem.
277
41410-41416
2002
Methanocaldococcus jannaschii
Steinbacher, S.; Schiffmann, S.; Richter, G.; Huber, R.; Bacher, A.; Fischer, M.
Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism
J. Biol. Chem.
278
42256-42265
2003
Methanocaldococcus jannaschii (Q60364)
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
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