Information on EC 6.3.3.3 - Dethiobiotin synthase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY
6.3.3.3
-
RECOMMENDED NAME
GeneOntology No.
Dethiobiotin synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
show the reaction diagram
the carbonylation of 7,8-diaminononanoic acid proceeds regiospecifically via the N7-carbamate
-
ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
show the reaction diagram
mechanistic model in which binding of Mg2+ and the triphosphate element of ATP to the enzyme creates the appropriate geometry for substrate 7,8-diaminononanoate-binding and carbamate formation
-
ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
show the reaction diagram
the final intermediate is the phosphoric acid anhydride of the carbamate
-
ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
show the reaction diagram
8-aminocarbamate of (7R,8S)-7,8 diaminononanoate is an enzyme-bound intermediate
-
ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
show the reaction diagram
enzyme reaction involves three steps: carbamylation of theN7 position of 7,8-diaminononanoate, formation of a carbamate-phosphoric anhydride intermediate, and, closure of the ureido ring to form dethiobiotin and release of the inorganic phosphate
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
carboxylation
-
-
-
-
heteroatomic ring closure
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
biotin biosynthesis from 8-amino-7-oxononanoate I
-
biotin biosynthesis from 8-amino-7-oxononanoate II
-
Biotin metabolism
-
Metabolic pathways
-
SYSTEMATIC NAME
IUBMB Comments
7,8-Diaminononanoate:carbon-dioxide cyclo-ligase (ADP-forming)
CTP has half the activity of ATP.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Desthiobiotin synthetase
-
-
-
-
Dethiobiotin synthase
-
-
-
-
Dethiobiotin synthetase
-
-
-
-
Dethiobiotin synthetase
Q6NQL9
-
DTB synthetase
-
-
-
-
DTBS
-
-
-
-
Synthetase, dethiobiotin
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
37259-75-9
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
BIO3; gene bio3
Q6NQL9
UniProt
Manually annotated by BRENDA team
Bacillus roseus
-
-
-
Manually annotated by BRENDA team
active site mutant enzymes: T11V, E12A, E12D, K15Q, K37L, K37Q, K37R, S41A, S41C, overproduced in Escherichia coli strain lacking a functional endogenous DTBS
-
-
Manually annotated by BRENDA team
Pseudomonas graveolens
-
-
-
Manually annotated by BRENDA team
Saccharomyces kloeckerianus
-
-
-
Manually annotated by BRENDA team
D-biotin-overproducing strain
-
-
Manually annotated by BRENDA team
Sporobolomyces coprophilus
-
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP + 7,8-diaminononanoate + CO2
AMP + phosphate + dethiobiotin
show the reaction diagram
Pseudomonas graveolens
-
not
-
-
-
ADP + 7,8-diaminononanoate + CO2
AMP + phosphate + dethiobiotin
show the reaction diagram
Lysinibacillus sphaericus, Lysinibacillus sphaericus IFO 3525
-
5% of the activity relative to ATP
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Saccharomyces kloeckerianus, Lipomyces starkeyi, Sporidiobolus salmonicolor, Sporobolomyces coprophilus, Rhodotorula glutinis, Klebsiella pneumoniae, Bacillus roseus
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Q6NQL9
-
-
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
penultimate step in biotin biosynthesis
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
penultimate step in biotin biosynthesis
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
penultimate step in biotin biosynthesis
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Q6NQL9
third step in the biosynthesis of biotin, overview
-
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Lysinibacillus sphaericus IFO 3525
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Bacillus subtilis IAM 1193
-
-
-
-
ATP + 7,8-diaminononanoate + CO2
?
show the reaction diagram
-
penultimate enzyme of biotin biosynthesis
-
-
-
ATP + diaminobiotin + CO2
ADP + phosphate + biotin
show the reaction diagram
-
-
-
-
ATP + diaminobiotin + CO2
ADP + phosphate + biotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
-
ATP + diaminobiotin + CO2
ADP + phosphate + biotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
ATP + diaminobiotin + CO2
ADP + phosphate + biotin
show the reaction diagram
-
37% of the activity relative to 7,8-diaminononanoate
-
-
-
CTP + 7,8-diaminononanoate + CO2
CDP + phosphate + dethiobiotin
show the reaction diagram
-
-
-
-
-
CTP + 7,8-diaminononanoate + CO2
CDP + phosphate + dethiobiotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
-
CTP + 7,8-diaminononanoate + CO2
CDP + phosphate + dethiobiotin
show the reaction diagram
-
50% of the activity relative to ATP
-
-
-
GTP + 7,8-diaminononanoate + CO2
GDP + phosphate + dethiobiotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
-
ITP + 7,8-diaminononanoate + CO2
IDP + phosphate + dethiobiotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
-
ITP + 7,8-diaminononanoate + CO2
IDP + phosphate + dethiobiotin
show the reaction diagram
Lysinibacillus sphaericus, Lysinibacillus sphaericus IFO 3525
-
8.6% of the activity relative to ATP
-
-
-
UTP + 7,8-diaminononanoate + CO2
UDP + phosphate + dethiobiotin
show the reaction diagram
Pseudomonas graveolens
-
-
-
-
-
UTP + 7,8-diaminononanoate + CO2
UDP + phosphate + dethiobiotin
show the reaction diagram
Lysinibacillus sphaericus, Lysinibacillus sphaericus IFO 3525
-
7% of the activity relative to ATP
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
penultimate step in biotin biosynthesis
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
penultimate step in biotin biosynthesis
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
-
penultimate step in biotin biosynthesis
-
?
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
Q6NQL9
third step in the biosynthesis of biotin, overview
-
-
?
ATP + 7,8-diaminononanoate + CO2
?
show the reaction diagram
-
penultimate enzyme of biotin biosynthesis
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Fe2+
Pseudomonas graveolens
-
71-91% of the activity relative to Mg2+
Mg2+
-
Km: 40 mM MgCl2; required
Mg2+
-
required
Mg2+
Pseudomonas graveolens
-
required
Mg2+
-
essential cofactor for both substrate binding and carbamate formation
Mn2+
Pseudomonas graveolens
-
95-136% of the activity relative to Mg2+
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1,10-phenanthroline
Pseudomonas graveolens
-
-
2,2'-dipyridyl
Pseudomonas graveolens
-
-
6-hydroxypyrimidin-4(3H)-one
-
competitive inhibition
7,8-diaminononanoate
Pseudomonas graveolens
-
competitive to diaminobiotin
ADP
-
competitive to ATP
ADP
Pseudomonas graveolens
-
competitive to ATP
Ag+
-
1 mM, 100% inhibition
Cd2+
-
1 mM, 70% inhibition
Co2+
-
1 mM, 35% inhibition
Cu2+
-
1 mM, 100% inhibition
dethiobiotin
-
10 mM, 30% inhibition
Diaminobiotin
Pseudomonas graveolens
-
competitive to 7,8-diaminononanoate
EDTA
Pseudomonas graveolens
-
-
Hg2+
-
1 mM, 100% inhibition
Ni2+
-
1 mM, 80% inhibition
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0013
-
7,8-diaminononanoate
-
-
0.002
-
7,8-diaminononanoate
-
pH 7.5, temperature not specified in the publication
0.045
-
7,8-diaminononanoate
-
-
0.029
-
ATP
-
pH 7.5, temperature not specified in the publication
additional information
-
additional information
-
-
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
11.2
-
6-hydroxypyrimidin-4(3H)-one
-
25C, pH 7.8
2.2
-
adenine
-
25C, pH 7.8
0.05
-
AMP-PNP
-
25C, pH 7.8
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.002
-
-
-
additional information
-
-
-
additional information
-
-
-
additional information
-
Pseudomonas graveolens
-
-
additional information
-
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
8
Pseudomonas graveolens
-
-
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
50
55
Pseudomonas graveolens
-
-
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Q6NQL9
BIO3 protein contains an N-terminal sequence that is predicted to target the protein to mitochondria
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
42000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 25000, calculation from nucleotide sequence
dimer
-
2 * 24500, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
at 1.65 A resolution
-
crystallographic studies of complexes with substrates and a reaction intermediate
-
crystals are grown from ammonium sulfate, crystals are soaked in the crystallisation-well solution plus 50 mM 6-hydroxypyrimidin-4(3H)-one for 1 hour, 6-hydroxypyrimidin-4(3H)-one is embedded in the base binding pocket of DTBS
-
hanging-drop vapor diffusion, 0.005 ml of well solution containing 100 mM magnesium acetate or MgCl2, 9-11% polyethylene glycol 8000 and 100 mM cacodylate, pH 6.5 are mixed with 0.002 ml protein solution containing 30 mg/ml DTBS, crystals grow within a week at 20C, crystals of DTBS complexed with diaminopelargonic acid-MgADP-AlF3 and with dethiobiotin-MgADP-phosphate, crystals diffract to 1.8 A
-
hanging-drop vapor diffusion, precipitant polyethylene glycol 8000, 100 mM cacodylate, pH 6.5, 200 mM magnesium acetate, crystals diffract to 0.97 A
-
X-ray crystallographic studies of the mutant enzymes S41A, S41C, K37Q, and K37L, show that the crystals are essentially isomorphous to that of the wild-type DTBS
-
in complexes with the substrate 7,8-diaminopelargonic acid or ADP and the product dethiobiotin, up to 1.85 A resolution.
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, 90% loss of activity after 24 h
-
4C, stable for about 2 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
active site mutant enzymes: T11V, E12A, E12D, K15Q, K37L, K37Q, K37R, S41A, S41C, overproduced in Escherichia coli
-
recombinant DTBS, ammonium sulfate, Sephacryl S-200, Q-Sepharose
-
-
Pseudomonas graveolens
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
gene bio3, alleles bio1-3, bio2-3, and bio3-3, DNA and amino acid sequence determination and analysis and genotyping, encoded with gene bio1 in a bifunctional locus that catalyzes two sequential reactions in the same metabolic pathway via differential splicing, separate BIO3 and BIO1 transcripts and two different types of chimeric BIO3-BIO1 transcripts are produced. One of the fused transcripts is monocistronic and encodes a bifunctional fusion protein. A splice variant is bicistronic, with distinct but overlapping reading frames, overview
Q6NQL9
cloning of the biotin biosynthetic operon
-
overexpression in Escherichia coli
-
expression in Escherichia coli
-
nucleotide sequence
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
T11V
-
active site mutant enzymes: T11V, E12A, E12D, K15Q, K37L, K37Q, K37R, S41A, S41C, T11V mutant shows a 24000fold increase in the Km for ATP with little or no change in the Km for 7,8-diaminononanoate and in turnover number. Mutants E12A and E12D show wild-type activity with slightly elevated turnover numbers. Unlike wild-type enzyme mutant enzyme E12A has the same apparent Km at subsaturating and saturating ATP concentrations. Mutant enzymes K15Q, K37Q, and K37R have no catalytic activity. Mutant enzymes S41A and S41C have the same turnover number as the wild-type enzyme and a moderate increase in Km for ATP and 7,8-diaminononanoate
additional information
Q6NQL9
construction of bio3 insertion mutants, which have a similar phenotype to the bio1 and bio2 auxotrophs identified using forward genetic screens for arrested embryos rescued on enriched nutrient medium. Genes bio3 and bio1 mutants define a single genetic complementation group, separate BIO3 and BIO1 transcripts and two different types of chimeric BIO3-BIO1 transcripts are produced. One of the fused transcripts is monocistronic and encodes a bifunctional fusion protein. A splice variant is bicistronic, with distinct but overlapping reading frames. Dual functionality of the monocistronic transcript is confirmed by complementing the orthologous auxotrophs of Escherichia coli strain. Allelism between bio1 and bio3 heterozygotes and phenotypes, overview