The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.
The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.
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DOI：
10.2210/pdb1hut/pdb
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发表时间：
1994-06
期刊：
影响因子：
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通讯作者：
K. Padmanabhan;K. Padmanabhan;J. Ferrara;J. Sadler;A. Tulinsky
中科院分区：
文献类型：
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作者：
K. Padmanabhan;K. Padmanabhan;J. Ferrara;J. Sadler;A. Tulinsky
人 α-凝血酶和 GGTTGGTGTGGTTGG 15 核苷酸共有序列之间的复合物结构已通过 X 射线晶体学解析，并以 2.9-A 分辨率精修至 R 值 0.159。与在溶液中一样，在复合物中，单链 DNA 折叠成具有两个 G 四联体的结构。 DNA 夹在晶体结构中两个对称相关凝血酶分子的两个不同带正电区域之间，产生离子和疏水相互作用。一个区域是纤维蛋白原识别外部位点，另一个区域是推定的肝素结合位点。具有凝血酶Arg75-->Glu突变体的DNA 15聚体对纤维蛋白原凝固和血小板活化缺乏抑制作用与纤维蛋白原外位点中DNA的几个盐桥一致。 DNA 与邻近分子的肝素位点的结合似乎只是补偿残余电荷。复合物和 NMR 溶液结构之间 15 聚体环构象的差异可归因于凝血酶结合时的构象变化。尽管单价阳离子存在时有利于 G-四链体，但在凝血酶复合物中没有证据表明存在单价阳离子。
The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets. The DNA is sandwiched between two different positively charged regions of two symmetry-related thrombin molecules in the crystal structure making ionic and hydrophobic interactions. One region is the fibrinogen recognition exosite and the other, the putative heparin binding site. The lack of inhibition of fibrinogen clotting and platelet activation by the DNA 15-mer with the Arg75-->Glu mutant of thrombin is consistent with the several salt bridges of the DNA in the fibrinogen exosite. The association of DNA with the heparin site of a neighboring molecule appears to simply compensate residual charge. Differences in the 15-mer loop conformations between the complex and NMR solution structures can be attributed to conformational changes upon thrombin binding. Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the latter in the thrombin complex.