1d97
From Proteopedia
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CHIRAL PHOSPHOROTHIOATE ANALOGUES OF B-DNA: THE CRYSTAL STRUCTURE OF RP-D(GP(S) CPGP(S)CPGP(S)C)
Overview
The compound Rp-d[Gp(S)CpGp(S)CpGp(S)C], an analogue of the deoxyoligomer, d(G-C)3, crystallizes in space group P2(1)2(1)2(1) with a = 34.90 A, b =, 39.15 A and c = 20.64 A. The structure, which is not isomorphous with any, previously determined deoxyoligonucleotide, was refined to an R factor of, 14.5% at a resolution of 2.17 A, with 72 solvent molecules located. The, two strands of the asymmetric unit form a right-handed double helix, which, is a new example of a B-DNA conformation and brings to light an important, and overlooked component of flexibility of the double helix. This, flexibility is manifest in the alternation of the backbone conformation, between two states, defined by the adjacent torsion angles epsilon and, zeta, trans . gauche-(BI) and gauche-. trans (BII). BI is characteristic, of classical of B-DNA and has an average C(1') to C(1') separation of 4.5, A. The corresponding separation for BII is 5.3 A. Each state is associated, with a distinct phosphate orientation where the plane of the PO2 (or POS), group is alternately near horizontal or vertical with respect to the helix, axis. The BI and BII conformations are out of phase on the two strands. As, a consequence, on one strand purine-pyrimidine stacking is better than, pyrimidine-purine, while the converse holds for the other strand. At each, base-pair step, good and bad stacking alternate across the helix axis. The, pattern of alternation is regular in the context of a fundamental, dinucleotide repeat. Re-examination of the B-DNA dodecamer, d(C-G-C-G-A-A-T-T-C-G-C-G) shows that the C-G-C-G regions contain the BI, and BII conformations, and the associated dual phosphate orientation and, asymmetric base stacking. Different mechanisms are used in the two, structures to avoid clashes between guanine residues on opposite strands, a combination of lateral slide, tilt and helical twist in the present, structure, and base roll, tilt and longitudinal slide (Calladine rules) in, the dodecamer. The flexibility of the phosphate orientations demonstrated, in this structure is important, since it offers a structural basis for, protein-nucleic acid recognition.
About this Structure
1D97 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]., Cruse WB, Salisbury SA, Brown T, Cosstick R, Eckstein F, Kennard O, J Mol Biol. 1986 Dec 20;192(4):891-905. PMID:3108513
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