6PVX

RNase A in complex with p5U

Summary for 6PVX

• Entry DOI: 10.2210/pdb6pvx/pdb
• Descriptor: Ribonuclease pancreatic, 5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine (3 entities in total)
• Functional Keywords: rnase a, nucleotide, poly-phosphate, lyase
• Biological source: Bos taurus (Bovine)
• Total number of polymer chains: 2
• Total formula weight: 29348.95

Authors

Windsor, I.W.,Sheppard, S.M.,Cummins, C.C.,Raines, R.T. (deposition date: 2019-07-21, release date: 2019-11-06, Last modification date: 2024-10-16)

Primary citation

Shepard, S.M.,Windsor, I.W.,Raines, R.T.,Cummins, C.C.
Nucleoside Tetra- and Pentaphosphates Prepared Using a Tetraphosphorylation Reagent Are Potent Inhibitors of Ribonuclease A.
J.Am.Chem.Soc., 141:18400-18404, 2019

PubMed Abstract: Adenosine and uridine 5'-tetra- and 5'-pentaphosphates were synthesized from an activated tetrametaphosphate ([PPN][PO], [PPN][], PPN = bis(triphenylphosphine)iminium) and subsequently tested for inhibition of the enzymatic activity of ribonuclease A (RNase A). Reagent [PPN][] reacts with unprotected uridine and adenosine in the presence of a base under anhydrous conditions to give nucleoside tetrametaphosphates. Ring opening of these intermediates with tetrabutylammonium hydroxide ([TBA][OH]) yields adenosine and uridine tetraphosphates (, ) in 92% and 85% yields, respectively, from the starting nucleoside. Treatment of ([PPN][]) with AMP or UMP yields nucleoside-monophosphate tetrametaphosphates () having limited aqueous stability. Ring opening of these ultraphosphates with [TBA][OH] yields and in 58% and 70% yield from AMP and UMP, respectively. We characterized inorganic and nucleoside-conjugated linear and cyclic oligophosphates as competitive inhibitors of RNase A. Increasing the chain length in both linear and cyclic inorganic oligophosphates resulted in improved binding affinity. Increasing the length of oligophosphates on the 5' position of adenosine beyond three had a deleterious effect on binding. Conversely, uridine nucleotides bearing 5' oligophosphates saw progressive increases in binding with chain length. We solved X-ray cocrystal structures of the highest affinity binders from several classes. The terminal phosphate of binds in the P enzymic subsite and forces the oligophosphate to adopt a convoluted conformation, while the oligophosphate of binds in several extended conformations, targeting multiple cationic regions of the active-site cleft.

PubMed: 31651164
DOI: 10.1021/jacs.9b09760

Experimental method

X-RAY DIFFRACTION (1.55 Å)