Stereochemistry of actinomycin binding to DNA: I. Refinement and further structural details of the actinomycin—deoxyguanosine crystalline complex

Abstract

Actinomycin D co-crystallizes with deoxyguanosine to form a 1:2 stoichiometric complex. The crystals are orthorhombic, space group P2 12 12 1, with cell parameters, a = 24.78, b = 29.47 and c = 13.60 A ̊ . The structure contains 140 atoms in the asymmetric unit (one actinomycin, two deoxyguanosine, and twelve water molecules) and has been solved using a combination of Patterson and tangent refinement methods, and refined by full matrix least squares to a residual of 9.4%. The two polypeptide chains of actinomycin are related by an approximate dyad axis lying roughly along a vector connecting the ON bridging atoms in the phenoxazone ring. A strong hydrogen bond exists between neighboring cyclic pentapeptide chains connecting the NH of one d-valine residue with the carbonyl oxygen of the other d-valine residue (2.94, 2.96 Å). The conformations of the peptide linkages are as follows: l-threonine- d-valine, trans; d-valine- lproline, cis; l-proline-sarcosine, cis; sarcosine- l-methylvaline, trans; l-threonine-carboxamide carbonyl oxygen and carbon of chromophore, trans. The 1:2 stoichiometry of the complex is a direct consequence of the 2-fold symmetry of actinomycin and reflects the two chemically equivalent binding sites available to deoxyguanosine for complex formation. The two deoxyguanosine molecules interact with each cyclic peptide residue and stack on alternate sides of the phenoxazone ring system. A strong hydrogen bond (2.82, 2.80 Å) connects the guanine 2-amino group with the carbonyl oxygen of the l-threonine residue, while a weaker hydrogen bond connects the guanine N (3) ring nitrogen with the NH group on this same l-threonine residue (3.15, 3.25 Å). Further details of the crystal structure are presented. This structure is an example of a protein—nucleic acid co-crystallization and the configuration observed in the crystalline complex explains in a natural way the stereochemistry of actinomycin binding to DNA. This is described in the accompanying paper.