Kim K H, Pan Z X, Honzatko R B, Ke H M, Lipscomb W N
Iowa State University, Department of Biochemistry and Biophysics, Ames 50011.
J Mol Biol. 1987 Aug 20;196(4):853-75. doi: 10.1016/0022-2836(87)90410-4.
The protein and solvent structure of the CTP-liganded form of aspartate carbamoyltransferase from Escherichia coli yields an R-factor of 0.155 for data to a resolution of 2.6 A. The model has 7353 protein atoms, 945 sites for solvent, and two molecules of CTP. A total of 25 of the 912 residues of the model exist in more than one conformation. The root-mean-square deviation of bond lengths and angles from their ideal values is 0.013 A and 2.1 degrees, respectively. The model reported here reflects a correction in the trace of the regulatory chain. One molecule of CTP binds to each of the two regulatory chains of the asymmetric unit of the crystal. The interactions between the pyrimidine of each CTP molecule and the protein are similar. The 4-amino group of CTP binds to the carbonyl groups of residues 89 (tyrosine) and 12 (isoleucine) of the regulatory chain. The nitrogen of position 3 of the pyrimidine binds to the amide group of residue 12; the 2-keto group binds to lysine 60. The 2'-OH group of the ribose forms hydrogen bonds with lysine 60 and the carbonyl group of residue 9 (valine). The binding of the phosphate groups of CTP to the regulatory chain probably reflects an incomplete association of CTP with the enzyme at pH 5.8. A lattice contact influences the interaction between the triphosphate group of one CTP molecule and the protein. For the other CTP molecule, only lysine 94 binds to the phosphate groups of CTP. Of the two regulatory and two catalytic chains of the asymmetric unit of the crystal, there are only two significant violations of non-crystallographic symmetry. The active site in the vicinity of arginine 54 of one catalytic chain is larger than the active site of its non-crystallographic mate. The "expanded" cavity accommodates four solvent molecules in the vicinity of arginine 54 as opposed to two molecules of water for the "contracted" cavity. Furthermore, arginine 54 in the "expanded" pocket adopts two conformations, either hydrogen-bonding to glutamate 86 or to the phenolic oxygen atom of tyrosine 98; residues 86 and 98 are in a catalytic chain related by 3-fold symmetry to the catalytic chain of arginine 54. In the "contracted" pocket, arginine 54 binds only to glutamate 86.(ABSTRACT TRUNCATED AT 400 WORDS)
来自大肠杆菌的天冬氨酸氨甲酰基转移酶CTP配体形式的蛋白质和溶剂结构，对于分辨率为2.6埃的数据，其R因子为0.155。该模型有7353个蛋白质原子、945个溶剂位点和两个CTP分子。模型的912个残基中共有25个存在不止一种构象。键长和键角与其理想值的均方根偏差分别为0.013埃和2.1度。此处报道的模型反映了调节链迹线的校正。一个CTP分子与晶体不对称单元的两条调节链中的每一条结合。每个CTP分子的嘧啶与蛋白质之间的相互作用相似。CTP的4-氨基与调节链中第89位（酪氨酸）和第12位（异亮氨酸）残基的羰基结合。嘧啶第3位的氮与第12位残基的酰胺基结合；2-酮基与赖氨酸60结合。核糖的2'-羟基与赖氨酸60和第9位（缬氨酸）残基的羰基形成氢键。CTP的磷酸基团与调节链的结合可能反映了在pH 5.8时CTP与酶的不完全结合。一种晶格接触影响一个CTP分子的三磷酸基团与蛋白质之间的相互作用。对于另一个CTP分子，只有赖氨酸94与CTP的磷酸基团结合。在晶体不对称单元的两条调节链和两条催化链中，只有两个显著违反非晶体学对称性的情况。一条催化链中精氨酸54附近的活性位点比其非晶体学配对的活性位点大。“扩展”的腔在精氨酸54附近容纳四个溶剂分子，而“收缩”的腔容纳两个水分子。此外，“扩展”口袋中的精氨酸54有两种构象，要么与谷氨酸86氢键结合，要么与酪氨酸98的酚氧原子氢键结合；第86位和第98位残基在一条与精氨酸54的催化链具有三重对称性的催化链中。在“收缩”口袋中，精氨酸54仅与谷氨酸86结合。（摘要截于400字）
