Ribose-phosphate diphosphokinase is an enzyme that converts ribose 5-phosphate into phosphoribosyl pyrophosphate. It is classified under EC126.96.36.199, ribose 5-phosphate is produced by the HMP Shunt Pathway from Glucose-6-Phosphate. The product phosphoribosyl pyrophosphate acts as a component of the purine salvage pathway. Dysfunction of the enzyme would thereby undermine purine metabolism, ribose-phosphate pyrophosphokinase exists in bacteria, plants, and animals, and there are three isoforms of human ribose-phosphate pyrophosphokinase. In humans, the genes encoding the enzyme are located on the X chromosome, ribose-phosphate diphosphokinase transfers the diphosphoryl group from Mg-ATP to ribose 5-phosphate. The enzymatic reaction begins with the binding of ribose 5-phosphate, followed by binding of Mg-ATP to the enzyme, in the transition state upon binding of both substrates, the diphosphate is transferred. The enzyme first releases AMP before releasing the product phosphoribosyl pyrophosphate, crystallization and X-ray diffraction studies elucidated the structure of the enzyme, which was isolated by cloning, protein expression, and purification techniques. One subunit of ribose-phosphate diphosphokinase consists of 318 amino acids, the enzyme complex consists of three homodimers. The catalytic site of the enzyme binds ATP and ribose 5-phosphate, the flexible loop, pyrophosphate binding loop, and flag region comprise the ATP binding site, located at the interface between two domains of one subunit. The flexible loop is so named because of the its large variability in conformation, the ribose 5-phosphate binding site consists of residues Asp220–Thr228, located in the C-terminal domain of one subunit. The allosteric site, which binds ADP, consists of amino acid residues from three subunits, the product of this reaction, phosphoribosyl pyrophosphate, is used in numerous biosynthesis pathways. PRPP provides the ribose sugar in de novo synthesis of purines and pyrimidines, PRPP reacts with orotate to form orotidylate, which can be converted to uridylate. UMP can then be converted to the nucleotide cytidine triphosphate, the reaction of PRPP, glutamine, and ammonia forms 5-Phosphoribosyl-1-amine, a precursor to inosinate, which can ultimately be converted to adenosine triphosphate or guanosine triphosphate. PRPP plays a role in purine salvage pathways by reacting with free purine bases to form adenylate, guanylate, PRPP is also used in the synthesis of NAD, the reaction of PRPP with nicotinic acid yields the intermediate nicotinic acid mononucleotide. Ribose-phosphate diphosphokinase requires Mg2+ for activity, the acts only on ATP coordinated with Mg2+. Ribose-phosphate diphosphokinase is regulated by phosphorylation and allostery and it is activated by phosphate and inhibited by ADP, it is suggested that phosphate and ADP compete for the same regulatory site. At normal concentrations, phosphate activates the enzyme by binding to its allosteric regulatory site, however, at high concentrations, phosphate is shown to have an inhibitory effect by competing with the substrate ribose 5-phosphate for binding at the active site. ADP is the key allosteric inhibitor of ribose-phosphate diphosphokinase and it has been shown that at lower concentrations of the substrate ribose 5-phosphate, ADP may inhibit the enzyme competitively
Phosphoribosyl pyrophosphate synthase 1, hexamer, Human
Overall reaction for phosphoribosyl pyrophosphate synthetase
SN2 mechanism of phosphoribosyl pyrophosphate synthetase
PyMol rendering of one subunit of the enzyme phosphoribosyl pyrophosphate synthetase I (human). Flexible loop colored in green; ribose 5-phosphate binding region colored in blue.