3LPN

Crystal structure of the phosphoribosylpyrophosphate (PRPP) synthetase from Thermoplasma volcanium in complex with an ATP analog (AMPCPP).

Summary for 3LPN

• Entry DOI: 10.2210/pdb3lpn/pdb
• Related: 1IBS 1U9Y 1U9Z 2H06 2HCR
• Descriptor: Ribose-phosphate pyrophosphokinase, DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, SULFATE ION, ... (4 entities in total)
• Functional Keywords: phosphoribosyltransferase, atp analog binding, atp-binding, kinase, metal-binding, nucleotide biosynthesis, nucleotide-binding, transferase
• Biological source: Thermoplasma volcanium
• Cellular location: Cytoplasm : Q97CA5
• Total number of polymer chains: 2
• Total formula weight: 65933.61

Authors

Cherney, M.M.,Cherney, L.T.,Garen, C.R.,James, M.N.G. (deposition date: 2010-02-05, release date: 2011-02-09, Last modification date: 2023-09-06)

Primary citation

Cherney, M.M.,Cherney, L.T.,Garen, C.R.,James, M.N.
The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs.
J.Mol.Biol., 413:844-856, 2011

PubMed Abstract: Phosphoribosyl pyrophosphate (PRPP) synthetase catalyzes the transfer of the pyrophosphate group from ATP to ribose-5-phosphate (R5P) yielding PRPP and AMP. PRPP is an essential metabolite that plays a central role in cellular metabolism. The enzyme from a thermophilic archaeon Thermoplasma volcanium (Tv) was expressed in Escherichia coli, crystallized, and its X-ray molecular structure was determined in a complex with its substrate R5P and with substrate analogs β,γ-methylene ATP and ADP in two monoclinic crystal forms, P2(1). The β,γ-methylene ATP- and the ADP-bound binary structures were determined from crystals grown from ammonium sulfate solutions; these crystals diffracted to 1.8 Å and 1.5 Å resolutions, respectively. Crystals of the ternary complex with ADP-Mg(2+) and R5P were grown from a polyethylene glycol solution in the absence of sulfate ions, and they diffracted to 1.8 Å resolution; the unit cell is approximately double the size of the unit cell of the crystals grown in the presence of sulfate. The Tv PRPP synthetase adopts two conformations, open and closed, at different stages in the catalytic cycle. The binding of substrates, R5P and ATP, occurs with PRPP synthetase in the open conformation, whereas catalysis presumably takes place with PRPP synthetase in the closed conformation. The Tv PRPP synthetase forms a biological dimer in contrast to the tetrameric or hexameric quaternary structures of the Methanocaldococcus jannaschii and Bacillus subtilis PRPP synthetases, respectively.

PubMed: 21963988
DOI: 10.1016/j.jmb.2011.09.007

Experimental method

X-RAY DIFFRACTION (1.8 Å)