X-ray Structures and Absolute Configurations of the Antibiotics Oligomycins A, B and C: Inhibitors of ATP Synthase

Abstract

Detailed X-ray structures are presented of the three chemical variants of the antibiotic Oligomycin (Oligomycins A, B and C), all inhibitors of the enzyme ATP synthase, which has itself been the subject of intensive studies in recent years. All three oligomycins crystallized in space group P2₁2₁2₁ with Z = 4 molecules per unit cell. Oligomycin A crystallized as the methanol solvate C₄₅H₇₂O₁₁ · CH₃OH with unit cell parameters a = 10.476(3), b = 17.342(1), c = 26.825(5) Å; oligomcin B as an acetic acid solvate C₄₅H₇₁O₁₂ · CH₃CO₂ with unit cell parameters a = 10.351(3), b = 17.305(1), c = 26.929(5) Å; and oligomycin C, C₄₅H₇₄O_10, with unit cell parameters a = 10.385(2), b = 11.9510(9), c = 38.007(4) Å. Oligomycin A refined with final R indices [I > 2sigma(I)], R1 = 0.0734, wR2 = 0.1940 and R indices (all data) R1 = 0.1106, wR2 = 0.2100 and absolute structure parameter = −0.7(4); for oligomycin B, final R indices [I > 2sigma(I)] are R1 = 0.0479, wR2 = 0.1388 and R indices (all data) are R1 = 0.0581, wR2 = 0.1435 and absolute structure parameter = −0.2(2); for oligomycin C, final R indices [I > 2sigma(I)] are R1 = 0.0454, wR2 = 0.1130 and R indices (all data) are R1 = 0.1061, wR2 = 0.1221 and absolute structure parameter = 0.1(3). The present study has resulted in providing: (1) corrections to the published chemical structures of the Oligomycins; (2) full descriptions of the absolute configurations; (3) information on regions of the structures with minor but important differences in their three dimensional structures which may create differences between the Oligomycins in their potential to bind to sites on the ATP synthase molecule. These results are all of major importance for future studies designed to establish details of the actual binding of Oligomycins to ATP synthase.

Index Abstract

Rex A. Palmer and Brian S. Potter

The antibiotics Oligomycin A, B and C are chemically very similar and all three are inhibitors of ATP synthases—enzymes, with complex multi-subunited protein structures, that can synthesize adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and inorganic phosphate. In mitochondria, the ATP synthase molecule can be visualized as having a major domain, F1,outside the cell membrane, and a minor domain, F_O, embedded within the membrane. F_O (written as a subscript “O”, not “zero”) which derives it name from being the Oligomycin binding domain and is also known as OSCP (the oligomycin sensitivity conferal protein).