Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.
Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.
复制标题
来自 Petromyzon marinus 的七鳃鳗血红蛋白分子模型的完善。
DOI：
10.1016/0022-2836(85)90049-x
复制
发表时间：
1985
影响因子：
5.6
通讯作者：
Love,WE
中科院分区：
文献类型：
--
作者：
Honzatko,RB;Hendrickson,WA;Love,WE
一个分子模型的蛋白质和环境溶剂的络合物的氰化物与高铁血红蛋白V从海lampreyPetromyzonmarinus产量的一个R-因子为0.142对X-射线衍射数据到2.0毫微米分辨率。与理想键长和键角的均方根差分别为0.014 °和1.5 °。属于平面群的原子偏离由最小二乘法确定的平面0.012 π。手性体积、肽扭转角和侧链扭转角的平均标准偏差分别为0.150 μ 3、2.0 °和19.4 °。多肽主链键合原子的热参数的均方根变化为1.21 Ω 2;侧链原子的热参数的变化为2.13 Ω 2。该模型包括蛋白质的149个氨基酸残基的11个侧链的多种构象。我们确定了231个位置的水分子在全部或部分占用的网站。这些位点的占据因子之和约为154，占晶体学不对称单元内550个水分子的28%。七鳃鳗高铁血红蛋白氰化物复合物中血红素的环境类似于哺乳动物四聚体的脱氧状态。特别是，近端组氨酸的原子NE 2与Fe之间的键距血红素平面的法线5.1 °。在脱氧血红蛋白和一碳氧血红蛋白中，与血红素平面法线的偏差分别为7 °至8 °和1 °。此外，近端组氨酸的原子CD 2与血红素C环的吡咯氮之间的距离（距离=3.29 π）和CEI与A环的吡咯氮之间的距离（距离= 3.06 π）的不相等是脱氧血红蛋白的特征，而不是碳一氧血红蛋白的特征，在这些距离相等的情况下。最后，在羰基111和酪氨酸149的羟基之间存在氢键。哺乳动物四聚体中相应的氢键是T到R状态转变的中心，存在于脱氧血红蛋白中，但不存在于碳一氧血红蛋白中。我们认为，低亲和力的氧七鳃鳗血红蛋白可能是这些T-状态的几何形状的后果。
A molecular model for the protein and ambient solvent of the complex of cyanide with methemoglobin V from the sea lampreyPetromyzon marinusyields anR-factor of 0.142 against X-ray diffraction data to 2.0 Å resolution. The root-mean-square discrepancies from ideal bond length and angle are, respectively, 0.014 Å and 1.5 °. Atoms that belong to planar groups deviate by 0.012 Å from planes determined by a least-squares procedure. The average standard deviation for chiral volumes, peptide torsion angle and torsion angles of side-chains are 0.150 Å3, 2.0 ° and 19.4 °, respectively. The root-mean-square variation in the thermal parameters of bonded atoms of the polypeptide backbone is 1.21 Å2; the variation in thermal parameters for side-chain atoms is 2.13 Å2. The model includes multiple conformations for 11 side-chains of the 149 amino acid residues of the protein. We identify 231 locations as sites of water molecules in full or partial occupancy. The sum of occupancy factors for these sites is approximately 154, representing 28% of the 550 molecules of water within the crystallographic asymmetric unit.The environment of the heme in the cyanide complex of lamprey methemoglobin resembles the deoxy state of the mammalian tetramer. In particular, the bond between atom NE2 of the proximal histidine and the Fe lies 5.1 ° from the normal of the heme plane. In deoxy- and carbonmonoxyhemoglobins, the deviations from the normal to the heme plane are 7 to 8 ° and 1 °, respectively. Furthermore, the inequality in the distance of atom CD2 of the proximal histidine from the pyrrole nitrogen of ring-Cof the heme (distance =3.29 å) and CEI from the pyrrole nitrogen of ring-A (distance = 3.06 Å) is characteristic of deoxyhemoglobin, not carbonmonoxyhemoglobin, where these distances are equal. Finally, a hydrogen bond exists between carbonyl 111 and the hydroxyl of tyrosine 149. The corresponding hydrogen link in the mammalian tetramer is central to the T to R state transition and is present in deoxyhemoglobin but absent in carbonmonoxyhemoglobin. We suggest that the low affinity of oxygen for lamprey hemoglobin may be a consequence of these T-state geometries.