Moréra S, Lascu I, Dumas C, LeBras G, Briozzo P, Véron M, Janin J
Laboratoire de Biologie Structurale, UMR 9920 CNRS-Université Paris-Sud, Gif-sur-Yvette, France.
Biochemistry. 1994 Jan 18;33(2):459-67. doi: 10.1021/bi00168a010.
The X-ray structure of nucleoside diphosphate kinase (NDP kinase) from the slime mold Dictyostelium discoideum has been determined to 2.2-A resolution and refined to an R-factor of 0.19 with and without bound ADP-Mg2+. The nucleotide binds near His 122, a residue which becomes phosphorylated during the catalytic cycle. The mode of binding is different from that observed in other phosphokinases, and it involves no glycine-rich sequence. The adenine base makes only nonpolar contacts with the protein. It points outside, explaining the lack of specificity of NDP kinase toward the base. The ribose 2'- and 3'-hydroxyls and the pyrophosphate moiety are H-bonded to polar side chains. A Mg2+ ion bridges the alpha- to the beta-phosphate which approaches the imidazole group of His 122 from the N delta side. The geometry at the active site in the ADP-Mg2+ complex suggests a mechanism for catalysis whereby the gamma-phosphate of a nucleoside triphosphate can be transferred onto His 122 with a minimum of atomic motion.
已测定盘基网柄菌核苷二磷酸激酶（NDP激酶）的X射线结构，分辨率达2.2埃，并在有无结合ADP-Mg2+的情况下将其精修至R因子为0.19。核苷酸结合在His 122附近，该残基在催化循环中会发生磷酸化。其结合模式与其他磷酸激酶中观察到的不同，且不涉及富含甘氨酸的序列。腺嘌呤碱基仅与蛋白质形成非极性接触。它向外指向，这解释了NDP激酶对碱基缺乏特异性的原因。核糖2'-和3'-羟基以及焦磷酸部分通过氢键与极性侧链相连。一个Mg2+离子桥接α-磷酸和β-磷酸，β-磷酸从Nδ侧接近His 122的咪唑基团。ADP-Mg2+复合物活性位点的几何结构表明了一种催化机制，通过该机制核苷三磷酸的γ-磷酸可以以最少的原子运动转移到His 122上。
