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Information on EC 4.1.99.12 - 3,4-dihydroxy-2-butanone-4-phosphate synthase and Organism(s) Candida albicans and UniProt Accession Q5A3V6

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.99 Other carbon-carbon lyases
                4.1.99.12 3,4-dihydroxy-2-butanone-4-phosphate synthase
IUBMB 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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Candida albicans
UNIPROT: Q5A3V6
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The taxonomic range for the selected organisms is: Candida albicans
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, atriba2, vdhbps, dihydroxybutanone phosphate synthase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3,4-dihydroxy-2-butanone 4-phosphate synthase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
show the reaction diagram
reaction mechanism, the enzyme possesses an essential acidic active-site loop
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) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
show the reaction diagram
D-ribulose 5-phosphate
formate + L-3,4-dihydroxybutan-2-one 4-phosphate
show the reaction diagram
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-ribulose 5-phosphate
formate + L-3,4-dihydroxy-2-butanone-4-phosphate
show the reaction diagram
the enzyme is involved in riboflavin biosynthesis
-
-
?
D-ribulose 5-phosphate
formate + L-3,4-dihydroxybutan-2-one 4-phosphate
show the reaction diagram
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
not involved in catalysis, stabilize the enzyme
Mg2+
essential for activity
Zn2+
not involved in catalysis, stabilize the enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.332
purified recombinant enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22530
2 * 22530, mass spectrometry, 2 * 22658, full-length enzyme, sequence calculation
22658
2 * 22530, mass spectrometry, 2 * 22658, full-length enzyme, sequence calculation
41000
recombinant enzyme, analytical ultracentrifugation, hydrodynamic studies
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 * 22530, mass spectrometry, 2 * 22658, full-length enzyme, sequence calculation
additional information
the enzyme possesses an essential acidic active-site loop, active site structure, structure comparisons, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant apoenzyme in complex with the substrate ribulose 5-phosphate, sitting drop vapour diffusion method, 0.003 ml of 17-34 mg/ml protein in 50 mM Tris-HCl, pH 7.5, is mixed with 0.001 ml of reservoir solution containing 85 mM sodium citrate, pH 5.0, and 17% PEG 8000, with or without 5 mM EDTA, equilibration against 0.3 ml reservoir solution, 0.003 ml of the complex solution is mixed with 0.001 ml of 90 mM Mes/NaOH, pH 6.0, containing 18% PEG 8000, addition of 2 mM D-ribulose 5-phosphate, 20°C, X-ray diffraction structure determination and analysis at 1.6-1.7 A resolution, molecular replacement, modelling
reinterpretation of the space-group symmetry is reported for two crystal structures, PDB codes 1tks and 1tku
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C59A
site-directed mutagenesis, the mutant shows 70% of wild-type enzyme activity
D92A
site-directed mutagenesis, inactive mutant
E166A
site-directed mutagenesis, inactive mutant
Q181R/Q183R
site-directed mutagenesis, construction of a synthetic gene, derived from orf 6.2440, with nucleotide exchanges at positions 414, 426, 477, 480, and 581
Y87A
site-directed mutagenesis, the mutant shows 2% of wild-type enzyme activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme, expressed from the synthetic gene in Escherichia coli, to homogeneity by hydrophobic interaction chromatography, ultrafiltration, and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
functional expression of the synthetic gene in Escherichia coli strains XL1-Blue and M15
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
the enzyme is a potential anti-infective target in the pathogenic yeast
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Echt, S.; Bauer, S.; Steinbacher, S.; Huber, R.; Bacher, A.; Fischer, M.
Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans
J. Mol. Biol.
341
1085-1096
2004
Candida albicans (Q5A3V6)
Manually annotated by BRENDA team
Le Trong, I.; Stenkamp, R.E.
Alternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase
Acta Crystallogr. Sect. D
64
219-220
2008
Candida albicans (Q5A3V6)
Manually annotated by BRENDA team