Lipanov A, Kopka M L, Kaczor-Grzeskowiak M, Quintana J, Dickerson R E
Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.
Biochemistry. 1993 Feb 9;32(5):1373-89. doi: 10.1021/bi00056a024.
For the first time, the same B-DNA oligomer has been crystallized and its structure solved in two different space groups. Crystallization of C-C-A-A-C-I-T-T-G-G with Ca2+ yields monoclinic space group C2 with a = 31.87 A, b = 25.69 A, c = 34.21 A, beta = 114.1 degrees, and five base pairs per asymmetric unit. The 5026 2 sigma data to 1.3 A refine to R = 0.152 with 72 waters, one heptavalent hydrated calcium complex, and one cacodylate ion per asymmetric unit. In contrast, crystallization with Mg2+ yields trigonal space group P3(2)21 with a = b = 33.23 A, c = 94.77 A, gamma = 120 degrees, and 10 base pairs per asymmetric unit. The 1725 2 sigma data to 2.2 A refine to R = 0.164 with 36 water molecules and one octahedral magnesium complex per asymmetric unit. The monoclinic form is virtually isostructural with previously solved monoclinic decamers, including twist angles of ca. 50 degrees at C-A and T-G steps. In contrast, the trigonal structure has quite different local helix parameters, with twist angles of ca. 36 degrees at the corresponding steps. These local parameter differences can only be attributed to crystal packing, suggesting that certain sequences of B-DNA are more flexible and influenced by their surroundings than had previously been thought. Such deformability may be important for interaction of B-DNA with control proteins, where both static structure and dynamic deformability comprise components of the recognition process. The crossing of two helices at an angle of 120 degrees in the trigonal cell is a model for an antiparallel, uncrossed Holliday junction, as has been noted earlier by Timsit and Moras [Timsit, Y., & Moras, D. (1991) J. Mol. Biol. 221, 919-940] from a rhombohedral DNA dodecamer structure analysis.
首次将相同的B - DNA寡聚物进行结晶，并在两种不同的空间群中解析其结构。C - C - A - A - C - I - T - T - G - G与Ca2+结晶得到单斜空间群C2，a = 31.87 Å，b = 25.69 Å，c = 34.21 Å，β = 114.1°，每个不对称单元有5个碱基对。5026个2σ数据至1.3 Å，用72个水分子、1个七价水合钙络合物和每个不对称单元1个二甲胂酸根离子精修后R = 0.152。相比之下，与Mg2+结晶得到三角空间群P3(2)21，a = b = 33.23 Å，c = 94.77 Å，γ = 120°，每个不对称单元有10个碱基对。1725个2σ数据至2.2 Å，用36个水分子和每个不对称单元1个八面体镁络合物精修后R = 0.164。单斜形式与先前解析的单斜十聚体几乎同构，包括在C - A和T - G步处约50°的扭转角。相比之下，三角结构具有相当不同的局部螺旋参数，在相应步处扭转角约为36°。这些局部参数差异只能归因于晶体堆积，这表明某些B - DNA序列比以前认为的更具柔性且受其周围环境影响。这种可变形性对于B - DNA与调控蛋白的相互作用可能很重要，其中静态结构和动态可变形性都是识别过程的组成部分。如Timsit和Moras [Timsit, Y., & Moras, D. (1991) J. Mol. Biol. 221, 919 - 940] 从菱形DNA十二聚体结构分析中较早指出的那样，三角晶胞中两个螺旋以120°角交叉是反平行、未交叉霍利迪连接体的模型。
