Recognition of RNase Sa by the Inhibitor Barstar: Structure of the Complex at 1.7 Å Resolution

Abstract

The 1.7 .~ resolution structure of RNase Sa complexed with the polypeptide inhibitor barstar is reported here. The crystals are in the hexagonal space group~ P65 with unit-cell dimensions a = b = 56.9, c = 135.8 A and the asymmetric unit contains one molecule of the complex. RNase Sa is an extracellular microbial ribonuclease produced by Streptomyces aureofaciens. Barstar is the natural inhibitor of barnase, the ribonuclease of Bacillus amyloliquefaciens. It inhibits RNase Sa and barnase in a similar manner by steric blocking of the active site. The structure of RNase Sa is very similar to that observed in crystals of the native enzyme and its complexes with nucleotides. Barstar retains the structure found in its complex with barnase. The accessible surface area of protein buried in the complex is about 300 ~2 smaller and there are fewer hydrogen bonds in the enzymeinhibitor interface in RNase Sa-barstar than in barnasebarstar, providing an explanation of the reduced binding affinity in the former. Previous studies of barstar complexes have used mutants of the inhibitor and this is the first structure which includes wild-type barstar.

Automated Prediction of Protein Association Rate Constants

“…This room is illustrated by comparing the complexes of barstar with barnase (1BRS; Table S1) and with ribonuclease Sa (1AY7; Table S2). The two nucleases are structurally similar (with a C α root-mean-square-deviation of 0.4 Å for 35 core residues), and their complexes with barstar are also similar (Sevcik et al, 1998). Correspondingly the basal rate constants, 9.2 × 10 4 to 7.9 × 10 4 M −1 s −1 , of the two complexes are also very similar.…”

X-ray Structure of Two Crystalline Forms of aStreptomycete Ribonuclease with Cytotoxic Activity

“…The yields range from 10 to 50 mg of protein/liter of culture medium (16). Barstar inhibits the enzymatic activity of Sa ribonucleases as it does barnase, its native partner, by sterically blocking the active site (17,18). Dissociation constants of the complexes of RNase Sa, Sa2, and Sa3 with barstar are 2 ϫ 10 Ϫ10 , 4 ϫ 10 Ϫ10 , and 2 ϫ 10 Ϫ12 M, respectively.…”

The development of an affinity evaluation and prediction system by using protein–protein docking simulations and parameter tuning

“…For these receptors, the score of each predicted ligand is not the maximum (ie, S PSC < 1.0) or the number of ligands with maximal score is not only one: 1AY732(index = 0), 1CAU33(2), 1D4V34(3), 1EAY35(4), 1EM836(5), 1VET37(11), 1WMH38(12), 1WRD39(13), 1XG240(14), 2F9Z41(16), 2HSN42(18), and 2NXN43(19). Thus, when using only the normalized S PSC , it is too difficult to evaluate and quantify the affinity between ligand and receptor.…”