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2.7.6.1: ribose-phosphate diphosphokinase

This is an abbreviated version!
For detailed information about ribose-phosphate diphosphokinase, go to the full flat file.

Word Map on EC 2.7.6.1

Reaction

ATP
+
D-ribose 5-phosphate
=
AMP
 +
5-phospho-alpha-D-ribose 1-diphosphate

Synonyms

5-phospho-alpha D-ribosyl 1-diphosphate synthase, 5-phosphoribose pyrophosphorylase, 5-phosphoribosyl-1-alpha-diphosphate synthase, 5-phosphoribosyl-1-pyrophosphate synthetase, 5-phosphoribosyl-alpha-1-pyrophosphate synthetase, AN6711.2, ATP: D-ribose-5-phosphate pyrophosphotransferase, ATP:D-ribose-5-phosphate pyrophosphotransferase, bsPRS, Pcal_1127, phosphoribosyl diphosphate synthase, phosphoribosyl pyrophosphate synthase 1 (PRS-1), phosphoribosyl pyrophosphate synthase enzyme, phosphoribosyl pyrophosphate synthetase, phosphoribosyl-1-pyrophosphate synthetase, phosphoribosyl-diphosphate synthetase, phosphoribosylpyrophosphate synthase, phosphoribosylpyrophosphate synthetase, phosphoribosylpyrophosphate synthetase 1, phosphoribosylpyrophosphate synthetase subunit 1, PP-ribose P synthetase, PPRibP synthetase, PRibPP synthase, PRPP synthase, PRPP synthetase, PRPPase, PRPPS, PRPPS1, PRPPS2, PRPS1, Prps1a, Prps1b, PRS, PRS-I, PRS1, Prs4, PrsA, PrsB, PrsC, pyrophosphokinase, ribose phosphate, pyrophosphoribosylphosphate synthetase, ribophosphate pyrophosphokinase, ribose-5-phosphate pyrophosphokinase, ribose-phosphate pyrophosphokinase, ribose-phosphate pyrophosphokinase 1, RPPK, SSO1045, TT_C1184, TT_C1274

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.6 Diphosphotransferases
                2.7.6.1 ribose-phosphate diphosphokinase

Crystallization

Crystallization on EC 2.7.6.1 - ribose-phosphate diphosphokinase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapour diffusion method
-
in combination with dynamic light scattering studies
-
in the presence of Mg2+
-
sitting drop vapor diffusion
-
X-ray diffraction
-
purified enzyme, hanging drop vapor diffusion technique by mixing of 0.001 ml of 10 mg/mL protein in 0.02 M Tris-HCl buffer, pH 7.5, containing 0.04% NaN3, with 0.001 ml of reservoir solution containing from 18% (NH4)2SO4, 0.02 M Tris-HCl buffer, pH 7.5, 0.02 mM MgCl2 and 0.02 mM ATP, screening and optimization to capillary counter-diffusion technique, largest crystals are obtained using a protein solution with a protein concentration of 14 mg/mL in 0.02 M Tris-HCl buffer, pH 7.5, containing 2 mM MgCl2, 2 mM ATP, and 0.04% NaN3, and a reservoir solution composed of 14% ammonium sulfate in 0.1 M Tris buffer, pH 8.5, containing 0.3 M NaCl, 2 mM MgCl2, and 0.04% NaN3, X-ray diffraction structure determination and analysis at 3.1 A resolution
structure to 2.71 A resolution, of single crystals grown under microgravity. The monomers are assembled into a hexamer with 32 point symmetry. The N-terminal regions of the subunits are located near the threefold axis and form a propeller-like structure in which each subunit interacts with two adjacent subunits in different manner
to 2.2 A resolution. The protein has two type I phosphoribosyltransferase folds, related by 2fold pseudosymmetry. The propeller-shaped homohexameric structure is composed of a trimer of dimers, with the C-terminal domains forming the dimeric blades of the propeller and the N-terminal domains forming the hexameric core. Several residues from a flexible loop occupy the site where the allosteric modulator, adenosine diphosphate, is predicted to bind
hanging-drop vapour diffusion method
purified recombinant enzyme in complex with Cd2+, ATP or sulfate, hanging drop vapour diffusion method, 20°C, X-ray diffraction structure determination and analysis at 2.20 A resolution
hanging-drop vapour-diffusion technique
to 0.98 A resolution, structural comparison with human enzyme
vapour diffusion sitting or hanging drop method. The protein is co-crystallised in the presence of AMP and D-ribose 5-phosphate, but in the electron density map of the active site only AMP and a sulphate ion are observed. Sulphate ion, reminiscent of the ammonium sulfate precipitation step of the purification, seems to bind tightly and, therefore, presumably occupies and blocks the D-ribose 5-phosphate binding site. The structure is determined at 2.8 A resolution
hanging-drop vapour-diffusion method. Orthorhombic system, with space group P2(1)2(1)2 and unit-cell parameters a = 213.2, b = 152.6, c = 149.3 A. The crystals diffract to a maximum resolution of 3.3 A
-
in complex with its substrate D-ribose 5-phosphate and with substrate analogs beta,gamma-methylene ATP and ADP, hanging drop vapor diffusion method, using 2 M ammonium sulfate, pH 4.0 or 30% (w/v) polyethylene glycol 600, pH 7.5
molecular dynamics simulation. With D-ribose 5-phosphate, phosphate forms hydrogen bonds with the carboxyl group of residue Asp220 and the main-chain N atoms of Ala226, Ser228, and Leu229. The residues Ser228 and Gly227 are linked to the oxygen atom of the carbohydrate ring. The hydroxyl group at the C1 atom of the ring forms hydrogen bonds with the nitrogen atoms and the hydroxyl oxygen atom of Thr225 and the nitrogen atoms of Ala226 and Gly227. ATP forms hydrogen bonds with the protein chains B and F and with D-ribose 5-phosphate
structure of crystals grown by the counter-diffusion method through a gel layer, to 3.0 A resolution. Space group P21, unit-cell parameters: a 107.7 A, b 112.6 A, c 110.2 A, alpha = gamma = 90°, beta = 116.6°
structure of recombinant enzyme at 2.2 A resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule is located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions are located in both the active and allosteric sites. The catalytic loop adopts different conformations in three independent subunits