Omichinski J G, Clore G M, Appella E, Sakaguchi K, Gronenborn A M
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892.
Biochemistry. 1990 Oct 9;29(40):9324-34. doi: 10.1021/bi00492a004.
The three-dimensional structure of a 30-residue synthetic peptide containing the carboxy-terminal "zinc finger" motif of a human enhancer binding protein has been determined by two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. The structure determination is based on 487 approximate interproton distance and 63 torsion angle (phi, psi, and chi 1) restraints. A total of 40 simulated annealing structures were calculated, and the atomic rms distribution about the mean coordinate positions (excluding residues 29 and 30 which are ill-defined) is 0.4 A for the backbone atoms, 0.8 A for all atoms, and 0.41 A for all atoms excluding the lysine and arginine side chains, which are disordered. The solution structure of the zinc finger consists of two irregular antiparallel beta-strands connected by an atypical turn (residues 3-12) and a classical alpha-helix (residues 14-24). The zinc is tetrahedrally coordinated to the sulfur atoms of two cysteines (Cys-5 and Cys-8) and to the N epsilon 2 atoms of two histidines (His-21 and His-27). The two cysteine residues are located in the turn connecting the two beta-strands (residues 5-8); one of the histidine ligands (His-21) is in the alpha-helix, while the second histidine (His-27) is at the end of a looplike structure (formed by the end of the alpha-helix and a turn). The general architecture is qualitatively similar to two previously determined low-resolution Cys2-His2 zinc finger structures, although distinct differences can be observed in the beta-strands and turn and in the region around the two histidines coordinated to zinc. Comparison of the overall polypeptide fold of the enhancer binding protein zinc finger with known structures in the crystallographic data base reveals a striking similarity to one region (residues 23-44) of the X-ray structure of proteinase inhibitor domain III of Japanese quail ovomucoid [Papamokos, E., Weber, E., Bode, W., Huber, R., Empie, M. W., Kato, I., & Laskowski, M. (1982) J. Mol. Biol. 158, 515-537], which could be superimposed with a backbone atomic rms difference of 0.95 A on residues 3-25 (excluding residue 6) of the zinc finger from the enhancer binding protein. The presence of structural homology between two proteins of very different function may indicate that the so-called zinc finger motif is not unique for a class of DNA binding proteins but may represent a general folding motif found in a variety of proteins irrespective of their function.
利用二维核磁共振（2D NMR）光谱法以及混合距离几何 - 动力学模拟退火计算，已确定了一种含有人增强子结合蛋白羧基末端“锌指”基序的30个残基合成肽的三维结构。结构测定基于487个近似质子间距离和63个扭转角（φ、ψ和χ1）约束条件。共计算了40个模拟退火结构，平均坐标位置周围的原子均方根偏差（不包括定义不明确的第29和30位残基），主链原子为0.4埃，所有原子为0.8埃，不包括无序的赖氨酸和精氨酸侧链的所有原子为0.41埃。锌指的溶液结构由两条不规则的反平行β链组成，通过一个非典型转角（第3 - 12位残基）和一个经典α螺旋（第14 - 24位残基）相连。锌以四面体方式与两个半胱氨酸（Cys - 5和Cys - 8）的硫原子以及两个组氨酸（His - 21和His - 27）的Nε2原子配位。两个半胱氨酸残基位于连接两条β链的转角处（第5 - 8位残基）；其中一个组氨酸配体（His - 21）在α螺旋中，而第二个组氨酸（His - 27）位于一个环样结构的末端（由α螺旋末端和一个转角形成）。总体结构在性质上与之前确定的两个低分辨率Cys2 - His2锌指结构相似，尽管在β链、转角以及与锌配位的两个组氨酸周围区域可观察到明显差异。将增强子结合蛋白锌指的整体多肽折叠与晶体学数据库中的已知结构进行比较，发现与日本鹌鹑卵类粘蛋白蛋白酶抑制剂结构域III的X射线结构的一个区域（第23 - 44位残基）[Papamokos, E., Weber, E., Bode, W., Huber, R., Empie, M. W., Kato, I., & Laskowski, M. (1982) J. Mol. Biol. 158, 515 - 537]有显著相似性，该区域与增强子结合蛋白锌指的第3 - 25位残基（不包括第6位残基）的主链原子均方根偏差为0.95埃。功能差异很大的两种蛋白质之间存在结构同源性，这可能表明所谓的锌指基序并非一类DNA结合蛋白所特有，而是可能代表了在多种蛋白质中发现的一种通用折叠基序，与它们的功能无关。
