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2.4.2.19: nicotinate-nucleotide diphosphorylase (carboxylating)

This is an abbreviated version!
For detailed information about nicotinate-nucleotide diphosphorylase (carboxylating), go to the full flat file.

Word Map on EC 2.4.2.19

Reaction

beta-nicotinate D-ribonucleotide
+
diphosphate
 +
CO2
=
pyridine-2,3-dicarboxylate
 +
5-phospho-alpha-D-ribose 1-diphosphate

Synonyms

BNA6, general stress protein 70 , GSP70 , Hp-QAPRTase, hQPRTase, M6_Spy1061, NAD pyrophosphorylase, NadC, nicotinate mononucleotide pyrophosphorylase (carboxylating) (EC 2.4.2.19), nicotinate-nucleotide pyrophosphorylase (carboxylating), nicotinate-nucleotide:pyrophosphate phospho-alpha-D-ribosyltransferase (decarboxylating), pyrophosphorylase, nicotinate mononucleotide (carboxylating), QAPRTase, QPRT, QPRTase, QPRTase , QPT, QPT1, QPT2, quinolate phosphoribosyltransferase, quinolinate phosphoribosyl transferase, quinolinate phosphoribosyltansferase, quinolinate phosphoribosyltransferase, quinolinate phosphoribosyltransferase (decarboxylating), quinolinate phosphoribosyltransferase 1, quinolinate phosphoribosyltransferase 2, quinolinate phosphoribosyltransferase [decarboxylating] , quinolinic acid phosphoribosyl transferase, quinolinic acid phosphoribosyltransferase, quinolinic phosphoribosyltransferase, sp.NadC, spNadC, TM1645, type II quinolic acid phosphoribosyltransferase, type II quinolinic acid phosphoribosyltransferase

ECTree

     2 Transferases
         2.4 Glycosyltransferases
             2.4.2 Pentosyltransferases
                2.4.2.19 nicotinate-nucleotide diphosphorylase (carboxylating)

Crystallization

Crystallization on EC 2.4.2.19 - nicotinate-nucleotide diphosphorylase (carboxylating)

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of Hp-QAPRTase with bound quinolinic acid, nicotinic acid mononucleotide, and phthalic acid. Hp-QAPRTase crystals are grown at 20°C using the hanging drop vapor diffusion method
hanging-drop vapor-diffusion method
-
apoenzyme and in complex with phthalic acid, sitting drop vapor diffusion method, using 50 mM MES pH 6.5, 0.1 M NaH2PO4, 0.1 M K H2PO4, and 1.6-2.1 M NaCl
apoenzyme and in complex with quinolinic acid or nicotinic acid mononucleotide, hanging drop vapor diffusion method, using
hanging-drop vapour-diffusion method, PEG MME 2K
-
PDB code: 2jbm (apo-hQPRTase), alpha/beta barrel fold (12 beta strands + 11 alpha helices) with N-terminal domain (residues 1-112, 279-291) and C-terminal domain (residues 113-278), similar to bacterial QPRTases (PDB: 1x1o), active site at alpha/beta open sandwich structure that faces an alpha/beta barrel of the adjacent subunit harbouring the quinolinic acid binding site (Arg102, Arg138, Arg161, Lys139, Lys171, pocket at the centre of the barrel), space group P2(1)2(1)2(1), unit-cell parameters: a = 111.5 A, b = 179.5 A, c = 194.7 A, 12 monomers in asymmetric unit arranged as 2 hexamers of D3 symmetry, sitting-drop vapour diffusion: 5 days, 20°C, 2 microlitre protein solution (10 mg/ml, pH7.5) + 2 microlitre precipitant (0.6 M potassium/sodium tartrate, 0.1 M sodium HEPES pH7.6), resolution of 2 A, phase determination using multiple wavelength anomalous diffraction on crystals of the Se-Met variant
hangig-drop vapor diffusion method, X-ray crystal structure of the apoenzyme is determined by multiple isomorphous replacement at 2.4 A resolution, complex with quinolinate, phthalate, nicotinate mononucleotideand ternary complex with phthalate and a substrate analog 5-phosphoribosyl-1-(beta-methylene)diphosphate
-
apo, quinolinate-bound, 5-phospho-alpha-D-ribose 1-diphosphate-bound, and phthalate-bound forms. Crystallized at room temperature by the hanging drop vapor diffusion method. Both apo and holo crystals belong to space group R32 (alpha = 90°, beta = 90°, and gamma = 120°). One molecule per asymmetric unit except in QAPRTase holophthalate crystals where two molecules are found. The unit cell dimensions are: a = b = 154.9 A and c = 68.9 A (apo), a = b = 154.8 A and c = 68.6 A (holoquinolinate), a = b = 154.9 A and c = 70.6 A (holo-5-phospho-alpha-D-ribose 1-diphosphate), a = b = 155.5 A and c = 121.1 A (holophthalate), a = b = 154.7 A and c = 69.3 A (holophthalate-5-phospho-alpha-D-ribose 1-diphosphate)
hanging-drop vapor-diffusion method, determination of crystal structure of the enzyme with bound quinolinate to 2.8 A resolution and with bound nicotinic acid mononucleotide
-
hanging or sitting drop vapor diffusion method, using 0.48 M ammonium sulfate, 25% (w/v) PEG 6000 and 0.1 M bis-Tris (pH 6.5)
hanging-drop vapour-diffusion method, PEG 8000
-
in complex with nicotinate mononucleotide, hanging drop vapor diffusion method, using 100 mM Tris-HCl, pH 8.0, 16-24% (w/v) PEG 8000, 150-200 mM ammonium acetate
M1KCW7
purified recombinant enzyme, hanging drop vapour diffusion method, 10 mg/ml protein, crystallization solution contains 10% PEG 6000, and 0.1 M MES, pH 6.0, X-ray diffraction structure determination and analysis at 2.5 A resolution, molecular replacement, model construction