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Information on EC 6.3.3.3 - dethiobiotin synthase and Organism(s) Escherichia coli and UniProt Accession P13000

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EC Tree
     6 Ligases
         6.3 Forming carbon-nitrogen bonds
             6.3.3 Cyclo-ligases
                6.3.3.3 dethiobiotin synthase
IUBMB Comments
CTP has half the activity of ATP.
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This record set is specific for:
Escherichia coli
UNIPROT: P13000
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
dethiobiotin synthetase, dethiobiotin synthase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Desthiobiotin synthetase
-
-
-
-
Dethiobiotin synthase
-
-
-
-
Dethiobiotin synthetase
-
-
-
-
DTB synthetase
-
-
-
-
Synthetase, dethiobiotin
-
-
-
-
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
heteroatomic ring closure
-
-
-
-
carboxylation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -
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
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + (7R,8S)-7,8-diaminopelargonic acid + NaHCO3
ADP + phosphate + dethiobiotin + Na+ + OH-
show the reaction diagram
-
-
-
?
CTP + (7R,8S)-7,8-diaminopelargonic acid + NaHCO3
CDP + phosphate + dethiobiotin + Na+ + OH-
show the reaction diagram
-
-
-
?
GTP + (7R,8S)-7,8-diaminopelargonic acid + NaHCO3
GDP + phosphate + dethiobiotin + Na+ + OH-
show the reaction diagram
-
-
-
?
ITP + (7R,8S)-7,8-diaminopelargonic acid + NaHCO3
IDP + phosphate + dethiobiotin + Na+ + OH-
show the reaction diagram
-
-
-
?
TTP + (7R,8S)-7,8-diaminopelargonic acid + NaHCO3
TDP + phosphate + dethiobiotin + Na+ + OH-
show the reaction diagram
-
-
-
?
UTP + (7R,8S)-7,8-diaminopelargonic acid + NaHCO3
UDP + phosphate + dethiobiotin + Na+ + OH-
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
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
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
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6-hydroxypyrimidin-4(3H)-one
-
competitive inhibition
adenine
-
-
AMP-PNP
-
-
dethiobiotin
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10 mM, 30% inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.015 - 0.019
(7R,8S)-7,8-diaminopelargonic acid
0.01 - 0.017
ATP
0.391 - 1.09
CTP
1.09 - 1.56
GTP
0.384 - 0.6
NaHCO3
0.0013
7,8-diaminononanoate
-
-
0.005
ATP
-
-
3.4
CO2
-
-
0.6
Mg2+
-
-
additional information
additional information
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.9 - 49
(7R,8S)-7,8-diaminopelargonic acid
18.1 - 38.6
ATP
19.1 - 28.1
CTP
16.3 - 29
GTP
15.4 - 38.4
NaHCO3
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
11.2
6-hydroxypyrimidin-4(3H)-one
-
25°C, pH 7.8
2.2
adenine
-
25°C, pH 7.8
0.05
AMP-PNP
-
25°C, pH 7.8
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.437
ATP
Escherichia coli
wild-type, pH 7.5, 37°C
5.752
CTP
Escherichia coli
wild-type, pH 7.5, 37°C
2
GTP
Escherichia coli
above 2.0, wild-type, pH 7.5, 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
24500
-
2 * 24500, SDS-PAGE
42000
-
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 23500, SDS-PAGE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with CTP, to 2.3 A resolution. The nucleoside base is stabilized in its pocket through hydrogen-bonding interactions with the protein backbone, rather than amino acid side chains. DTBS could utilise ATP, CTP, GTP, ITP, TTP, or UTP with similar Km and kcat values
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 20°C, 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
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
N175A
2.7fold decrease in Km value for CTP
N175G
no significant effects on Km value for ATP, CTP
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
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 90% loss of activity after 24 h
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4°C, stable for about 2 weeks
-
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
overexpression in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Izumi, Y.; Kano, Y.; Inagaki, K.; Kawase, N.; Tani, Y.; Yamada, H.
Characterization of biotin biosynthetic enzymes of Bacillus sphaericus: a dethiobiotin producing bacterium
Agric. Biol. Chem.
45
1983-1989
1981
Klebsiella aerogenes, Alcaligenes faecalis, Priestia megaterium, Bacillus roseus, Lysinibacillus sphaericus, Corynebacterium glutamicum, Escherichia coli, Klebsiella pneumoniae, Lipomyces starkeyi, Pseudomonas taetrolens, Rhodotorula glutinis, Saccharomyces kloeckerianus, Sporobolomyces coprophilus, Sporidiobolus salmonicolor
-
Manually annotated by BRENDA team
Eisenberg, M.A.; Krell, K.
Dethiobiotin synthetase
Methods Enzymol.
62
348-352
1979
Escherichia coli
Manually annotated by BRENDA team
Krell, K.; Eisenberg, M.A.
The purification and properties of dethiobiotin synthetase
J. Biol. Chem.
245
6558-6566
1970
Escherichia coli
Manually annotated by BRENDA team
Cheeseman, P.; Pai, C.H.
Partial purification and properties of D-desthiobiotin synthetase from Escherichia coli
J. Bacteriol.
104
726-733
1970
Escherichia coli
Manually annotated by BRENDA team
Alexeev, D.; Bury, S.M.; Boys, C.W.G.; Turner, M.A.; Sawyer, L.; Ramsey, A.J.; Baxter, H.C.; Baxter, R.L.
Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis
J. Mol. Biol.
235
774-776
1994
Escherichia coli
Manually annotated by BRENDA team
Gibson, K.J.; Lorimer, G.H.; Rendina, A.R.; Taylor, W.S.; Cohen, G.; Gatenby, A.A.; Payne, W.G.; Roe, D.C.; Lockett, B.A.; Nudelman, A.; Marcovici, D.; Nachum, A.; Wexler, B.A.; Marsilii, E.L.; Turner, I.M.; Laurie, D.H.; Kalbach, C.E.; Chi, H.
Dethiobiotin synthetase: the carbonylation of 7,8-diaminononanoic acid proceeds regiospecifically via the N7-carbamate
Biochemistry
34
10976-10984
1995
Escherichia coli
Manually annotated by BRENDA team
Schneider, G.; Lindqvist, Y.
Structure of ATP-dependent carboxylase, dethiobiotin synthase
Methods Enzymol.
279
376-385
1997
Escherichia coli
Manually annotated by BRENDA team
Alexeev, D.; Baxter, R.L.; Smekal, O.; Sawyer, L.
Substrate binding and carboxylation by dethiobiotin synthetase - a kinetic and X-ray study
Curr. Biol.
3
1207-1215
1995
Escherichia coli
Manually annotated by BRENDA team
Huang, W.; Lindqvist, Y.; Schneider, G.; Gibson, K.J.; Flint, D.; Lorimer, G.
Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution
Structure
2
407-414
1994
Escherichia coli
Manually annotated by BRENDA team
Baxter, R.L.; Baxter, H.C.
The mechanism of Escherichia coli dethiobiotin synthetase - a closure of the ureido ring of dethiobiotin involves formation of a carbamic-phosphate mixed anhydride
J. Chem. Soc. Chem. Commun.
1994
759-760
1994
Escherichia coli
-
Manually annotated by BRENDA team
Baxter, R.L.; Ramsey, A.J.; MxIver, L.A.; Baxter, H.C.
Mechanism of dethiobiotin synthetase - characterization of the 8-aminocarbamate of (7R,8S)-7,8-diaminononanoate as an enzyme-bound intermediate
J. Chem. Soc. Chem. Commun.
1994
559-560
1994
Escherichia coli
-
Manually annotated by BRENDA team
Yang, G.; Sandalova, T.; Lohman, K.; Lindqvist, Y.; Rendina, A.R.
Active site mutants of the Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties
Biochemistry
36
4751-4760
1997
Escherichia coli
Manually annotated by BRENDA team
Huang, W.; Jia, J.; Gibson, K.J.; Taylor, W.S.; Rendina, A.R.; Schneider, G.; Lindqvist, Y.
Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate
Biochemistry
34
10985-10995
1995
Escherichia coli
Manually annotated by BRENDA team
Sandalova, T.; Schneider, G.; Kack, H.; Lindqvist, Y.
Structure of dethiobiotin synthetase at 0.97 A resolution
Acta Crystallogr. Sect. D
55
610-624
1999
Escherichia coli
-
Manually annotated by BRENDA team
Kack, H.; Sandmark, J.; Gibson, K.J.; Schneider, G.; Lindqvist, Y.
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis
Protein Sci.
7
2560-2566
1998
Escherichia coli
Manually annotated by BRENDA team
Alexeev, D.; Baxter, R.L.; Campopiano, D.J.; McAlpine, R.S.; McIver, L.; Sawyer, L.
Rational design of an inhibitor of dethiobiotin synthetase; interaction of 6-hydroxypyrimidin-4(3H)-one with the adenine base binding site
Tetrahedron
54
15891-15898
1998
Escherichia coli
-
Manually annotated by BRENDA team
Salaemae, W.; Yap, M.Y.; Wegener, K.L.; Booker, G.W.; Wilce, M.C.; Polyak, S.W.
Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase
Tuberculosis
95
259-266
2015
Escherichia coli (P13000), Escherichia coli, Mycobacterium tuberculosis (P9WPQ5), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WPQ5)
Manually annotated by BRENDA team