Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Islam, Z.; Kumar, A.; Singh, S.; Salmon, L.; Karthikeyan, S.
    Structural basis for competitive inhibition of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Vibrio cholerae (2015), J. Biol. Chem., 290, 11293-11308 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.99.12 gene ribB, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Vibrio cholerae serotype O1

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.99.12 purified enzyme in apoform or in complex with inhibitor 4-phospho-D-erythronohydroxamic acid, or substrate and substrate plus metal ions, sitting drop vapor diffusion method, mixing of 0.001 ml of 20 mg/ml protein in 25 mM Tris-HCl, pH 8.0, with 0.01 ml crystallization solution, containing for the apo form enzyme 0.2 M Na2HPO4, pH 9.1, and 20% PEG 3350, for phosphate-bound enzyme 0.2 M NaH2PO4, pH 4.5 and 20% PEG 3350, the Ru5P and 4PEH complex crystals are obtained by mixing vDHBPS with 10 mM Ru5P or 4PEH and incubation for 30 min at 20°C, grown in 0.2 M Na2HPO4, pH 9.1 and 20% PEG3350, the enzyme-Ru5P-Zn2+ and enzyme-4PEH-Zn2+ complex crystals are obtained by soaking complex crystals in 100 mM ZnCl2 for 12 h at 20°C, X-ray diffraction structure determination and analysis at 1.96 A, 1.86 A, 1.59 A, and 2.04 A resolution, respectively, modelling Vibrio cholerae serotype O1

Protein Variants

EC Number Protein Variants Comment Organism
4.1.99.12 E39A site-directed mutagenesis, inactive mutant Vibrio cholerae serotype O1
4.1.99.12 E41A site-directed mutagenesis, the mutant is almost inactive Vibrio cholerae serotype O1
4.1.99.12 F139A site-directed mutagenesis, the mutant shows moderately reduced activity compared to the wild-type enzyme Vibrio cholerae serotype O1
4.1.99.12 H154A site-directed mutagenesis, inactive mutant Vibrio cholerae serotype O1
4.1.99.12 M84A site-directed mutagenesis, the mutant shows moderately reduced activity compared to the wild-type enzyme Vibrio cholerae serotype O1
4.1.99.12 N89A site-directed mutagenesis, the mutant shows unaltered activity compared to the wild-type enzyme Vibrio cholerae serotype O1
4.1.99.12 R61A site-directed mutagenesis, the mutant shows unaltered activity compared to the wild-type enzyme Vibrio cholerae serotype O1
4.1.99.12 S64A site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme Vibrio cholerae serotype O1
4.1.99.12 V98A site-directed mutagenesis, the mutant shows slightly reduced activity compared to the wild-type enzyme Vibrio cholerae serotype O1

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.1.99.12 4-phospho-D-erythronohydroxamic acid 4PEH, structure analogue of D-ribulose 5-phosphate, competitive inhibitor, 4PEH inhibits the catalytic activity of DHBPS as it is unable to form a proposed intermediate that is crucial for DHBPS activity Vibrio cholerae serotype O1

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.1.99.12 Mg2+ required Vibrio cholerae serotype O1
4.1.99.12 Zn2+ required, binding structure analysis Vibrio cholerae serotype O1

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.99.12 D-ribulose 5-phosphate Vibrio cholerae serotype O1
-
formate + L-3,4-dihydroxybutan-2-one 4-phosphate
-
?
4.1.99.12 D-ribulose 5-phosphate Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
formate + L-3,4-dihydroxybutan-2-one 4-phosphate
-
?

Organism

EC Number Organism UniProt Comment Textmining
4.1.99.12 no activity in Homo sapiens
-
-
-
4.1.99.12 Vibrio cholerae serotype O1 Q9KKP2
-
-
4.1.99.12 Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 Q9KKP2
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.99.12 recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and gel filtration, followed by ultrafiltration Vibrio cholerae serotype O1

Reaction

EC Number Reaction Comment Organism Reaction ID
4.1.99.12 D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate reaction mechanism, detailed overview Vibrio cholerae serotype O1

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.99.12 D-ribulose 5-phosphate
-
Vibrio cholerae serotype O1 formate + L-3,4-dihydroxybutan-2-one 4-phosphate
-
?
4.1.99.12 D-ribulose 5-phosphate
-
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 formate + L-3,4-dihydroxybutan-2-one 4-phosphate
-
?
4.1.99.12 additional information substrate binding structures, overview Vibrio cholerae serotype O1 ?
-
?
4.1.99.12 additional information substrate binding structures, overview Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 ?
-
?

Subunits

EC Number Subunits Comment Organism
4.1.99.12 dimer the hydrophobic residues at the dimeric interface play a role in dimer formation, whereas some of the active site residues at the dimeric interface play a role in the catalytic activity of vDHBPS Vibrio cholerae serotype O1
4.1.99.12 More DHBPS enzyme structure comparisons Vibrio cholerae serotype O1

Synonyms

EC Number Synonyms Comment Organism
4.1.99.12 3,4-dihydroxy-2-butanone-4-phosphate synthase
-
Vibrio cholerae serotype O1
4.1.99.12 DHBPS
-
Vibrio cholerae serotype O1
4.1.99.12 ribB
-
Vibrio cholerae serotype O1
4.1.99.12 vDHBPS
-
Vibrio cholerae serotype O1
4.1.99.12 vribB
-
Vibrio cholerae serotype O1

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.1.99.12 37
-
assay at Vibrio cholerae serotype O1

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.99.12 7.5
-
assay at Vibrio cholerae serotype O1

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
4.1.99.12 0.1
-
4-phospho-D-erythronohydroxamic acid pH 7.5, 37°C, recombinant His-tagged wild-type enzyme Vibrio cholerae serotype O1

General Information

EC Number General Information Comment Organism
4.1.99.12 additional information DHBPS enzyme structure comparisons, active site architecture of enzyme vDHBPS Vibrio cholerae serotype O1
4.1.99.12 physiological function enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes one of the two committed steps in the riboflavin pathway and converts D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone 4-phosphate and formate Vibrio cholerae serotype O1