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6.3.3.3: dethiobiotin synthase

This is an abbreviated version!
For detailed information about dethiobiotin synthase, go to the full flat file.

Word Map on EC 6.3.3.3

Reaction

ATP
+
7,8-diaminononanoate
 +
CO2
=
ADP
 +
phosphate
 +
dethiobiotin

Synonyms

BIO3, BioD, BioD1, Desthiobiotin synthetase, Dethiobiotin synthase, Dethiobiotin synthetase, DTB synthetase, DTBS, Synthetase, dethiobiotin

ECTree

     6 Ligases
         6.3 Forming carbon-nitrogen bonds
             6.3.3 Cyclo-ligases
                6.3.3.3 dethiobiotin synthase

Crystallization

Crystallization on EC 6.3.3.3 - dethiobiotin synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
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 20°C, 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
-
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
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 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
in complexes with the substrate 7,8-diaminopelargonic acid or ADP and the product dethiobiotin, up to 1.85 A resolution.
-