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 hide
6.3.3.3
-
RECOMMENDED NAME
GeneOntology No.
Dethiobiotin synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylation
-
-
-
-
heteroatomic ring closure
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
biotin biosynthesis
-
-
biotin biosynthesis from 8-amino-7-oxononanoate I
-
-
biotin biosynthesis from 8-amino-7-oxononanoate II
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Biotin metabolism
-
-
Metabolic pathways
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-
SYSTEMATIC NAME
IUBMB Comments
7,8-Diaminononanoate:carbon-dioxide cyclo-ligase (ADP-forming)
CTP has half the activity of ATP.
CAS REGISTRY NUMBER
COMMENTARY hide
37259-75-9
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
BIO3; gene bio3
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Bacillus roseus
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Pseudomonas graveolens
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Saccharomyces kloeckerianus
-
-
-
Manually annotated by BRENDA team
Sporobolomyces coprophilus
-
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP + 7,8-diaminononanoate + CO2
AMP + phosphate + dethiobiotin
show the reaction diagram
ATP + 7,8-diaminononanoate + CO2
?
show the reaction diagram
-
penultimate enzyme of biotin biosynthesis
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
ATP + diaminobiotin + CO2
ADP + phosphate + biotin
show the reaction diagram
CTP + 7,8-diaminononanoate + CO2
CDP + phosphate + dethiobiotin
show the reaction diagram
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
UTP + 7,8-diaminononanoate + CO2
UDP + phosphate + dethiobiotin
show the reaction diagram
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + 7,8-diaminononanoate + CO2
?
show the reaction diagram
-
penultimate enzyme of biotin biosynthesis
-
-
-
ATP + 7,8-diaminononanoate + CO2
ADP + phosphate + dethiobiotin
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
Pseudomonas graveolens
-
71-91% of the activity relative to Mg2+
Mn2+
Pseudomonas graveolens
-
95-136% of the activity relative to Mg2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
Pseudomonas graveolens
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-
2,2'-dipyridyl
Pseudomonas graveolens
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-
6-hydroxypyrimidin-4(3H)-one
-
competitive inhibition
7,8-diaminononanoate
Pseudomonas graveolens
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competitive to diaminobiotin
adenine
-
-
Ag+
-
1 mM, 100% inhibition
AMP-PNP
-
-
Cd2+
-
1 mM, 70% inhibition
Co2+
-
1 mM, 35% inhibition
Cu2+
-
1 mM, 100% inhibition
dethiobiotin
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10 mM, 30% inhibition
Diaminobiotin
Pseudomonas graveolens
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competitive to 7,8-diaminononanoate
EDTA
Pseudomonas graveolens
-
-
Hg2+
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1 mM, 100% inhibition
Ni2+
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1 mM, 80% inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0013 - 0.045
7,8-diaminononanoate
0.005 - 0.42
ATP
3.4 - 10
HCO3-
0.6
Mg2+
-
-
additional information
additional information
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-
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
11.2
6-hydroxypyrimidin-4(3H)-one
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25C, pH 7.8
2.2
adenine
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25C, pH 7.8
0.05
AMP-PNP
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25C, pH 7.8
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8
Pseudomonas graveolens
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50 - 55
Pseudomonas graveolens
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-
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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
UNIPROT
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)
Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
42000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x * 25000, calculation from nucleotide sequence
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
at 1.65 A resolution
-
crystallographic studies of complexes with substrates and a reaction intermediate
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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
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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
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hanging-drop vapor diffusion, precipitant polyethylene glycol 8000, 100 mM cacodylate, pH 6.5, 200 mM magnesium acetate, crystals diffract to 0.97 A
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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
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in complexes with the substrate 7,8-diaminopelargonic acid or ADP and the product dethiobiotin, up to 1.85 A resolution.
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 90% loss of activity after 24 h
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4C, stable for about 2 weeks
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
active site mutant enzymes: T11V, E12A, E12D, K15Q, K37L, K37Q, K37R, S41A, S41C, overproduced in Escherichia coli
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recombinant DTBS, ammonium sulfate, Sephacryl S-200, Q-Sepharose
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloning of the biotin biosynthetic operon
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expression in Escherichia coli
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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
nucleotide sequence
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overexpression in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
T11V
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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
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
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