Structure of prothrombin fragment 1 refined at 2.8 A resolution.
Structure of prothrombin fragment 1 refined at 2.8 A resolution.
复制标题
DOI：
10.1016/0022-2836(88)90565-7
复制
发表时间：
1988-08
影响因子：
5.6
通讯作者：
A. Tulinsky;C. Park;E. Skrzypczak‐Jankun
中科院分区：
文献类型：
--
作者：
A. Tulinsky;C. Park;E. Skrzypczak‐Jankun
凝血酶原片段 1 的结构通过结合使用溶剂平坦化的多个和单个同晶置换方法以 2.8 Å 分辨率（1 Å = 0.1 nm）解析，并通过限制最小二乘法（R = 0.24）（不包括溶剂）对分子几何形状和各个热参数使用相当严格的限制进行精炼。尽管内环也构成了折叠环结构的表面，但内环环具有比外环显着更低的B值。该表面形成其他三环的纤维蛋白结合位点的赖氨酸子位点。片段 1 的氢键网络和离子对相互作用似乎在三环结构的各个环之间保持了紧凑的折叠结构。另一方面，由于三环与其前面的 30 个残基之间只有一个氢键，因此表明 Gla 结构域具有与其晶体无序一致的相当大的灵活性。 Asn77 糖基化位点已定位到壳二糖，但 Asn101 处仅订购了一个 N-乙酰基葡萄糖胺。其他三环的赖氨酸结合位点区域在片段 1 中未正确发育，导致其缺乏赖氨酸/纤维蛋白亲和力。 11 个不同三环中的大多数保守序列与以下任一相关：（1）保护折叠所基于的内环二硫键 Cys87-127、Cys115-139；或（2）赖氨酸结合位点的要求。守恒的其余部分通常与折叠的十个反向转弯有关；在这 40 个残基（或大约序列的一半）中，有 14 个残基在 8 个不同的轮次中是保守的。分子间堆积由通过晶体学 43 螺旋轴相关的片段 1 分子的无限螺旋柱组成，这些螺旋柱通过来自不同分子的芳香族簇的范德华相互作用结合在一起，通过晶体学 2 倍旋转轴相关。
The structure of prothrombin fragment 1, solved at 2.8 Å resolution (1 Å = 0.1 nm) by a combination of multiple and single isomorphous replacement methods utilizing solvent flattening, has been refined by restrained least-squares methods (R= 0.24), solvent not included, using fairly stringent restraints on the molecular geometry and individual thermal parameters. The inner kringle loop possesses significantly lowerB-values than the outer loops even though the former also constitutes a surface of the folded kringle structure. This surface forms the Lys sub-site of the fibrin binding site of other kringles. The hydrogen bonding network and ion pair interactions of fragment 1 appear to maintain a compact folded structure among the various loops of the kringle structure. On the other hand, since there is only one hydrogen bond between the kringle and its preceding 30 residues, considerable flexibility is suggested for the Gla-domain consistent with its disorder in crystals. A chitobiose has been located at the Asn77 glycosylation site, but only a singleN-acetyl-glucosamine is ordered at Asn101. The lysine binding site region of other kringles is not properly developed in fragment 1, accounting for its lack of Lys/fibrin affinity. Most of the conserved sequence among 11 different kringles is associated with either: (1) protecting the inner loop disulfides Cys87–127, Cys115–139 upon which the folding is based; or (2) a requirement of the lysine binding site. The remainder of the conservation is generally associated with the ten reverse turns of the folding; of these 40 residues, or about half the sequence, 14 are conserved among eight different turns. The intermolecular packing consists of infinite helical columns of fragment 1 molecules related by a crystallographic 43screw axis, which are held together by van der Waals' interactions of aromatic clusters from different molecules related by a crystallographic 2-fold rotation axis.