PMID: 11856829 , Related PDB ids: 1KF2, 1KF3, IKF4, IKF5, IKF7, IKF8

Authors:

Berisio R, Sica F, Lamzin VS, Wilson KS, Zagari A, Mazzarella L

Title:

Atomic resolution structures of ribonuclease A at six pH values.

Journal:

Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):441-50. Epub 2002, Feb 21.

Abstract:

The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.