Ribonuclease structure and catalysis: crystal structure of sulfate-free native ribonuclease A at 1.5-A resolution

The structure of native bovine pancreatic ribonuclease A, without the inhibitory sulfate anion normally bound at the active site, has been determined by X-ray diffraction at 1.53-A resolution. Treatment of a crystal of ribonuclease containing sulfate with an alkaline buffer released most of the sulfate anions. On return to active pH, few of the side chains moved, and the backbone structure remained unchanged. The active site conformation was essentially unchanged except for the replacement of the sulfate anion by a water molecule, which is hydrogen-bonded to histidine-12 and to another water, and for a small movement of the side chain of lysine-41. Histidines-12 and -119, the catalytic basic and acidic residues, have not moved. Thus the distance between them, and the presence of an intervening water, prohibits the possibility of their being hydrogen-bonded together. The structure has been refined by restrained least squares to an R factor of 0.17. Analysis of individual atomic temperature factors indicates that the molecule has become less rigid in general but that some regions were particularly affected by loss of the sulfate, while others were relatively unaffected. The active site geometry of native ribonuclease A supports the original in-line mechanism of Rabin and co-workers and is in disagreement with the adjacent mechanism of Witzel and co-workers.