Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase
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DOI：
10.1093/nar/gkh212
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Stoddard, BL
中科院分区：
文献类型：
--
作者：
Eastberg, JH;Pelletier, J;Stoddard, BL
T4噬菌体多核苷酸激酶(PNK)具有5‘-羟基激酶、3’-磷酸酶和2‘，3’-环磷酸二酯酶活性。该酶磷酸化多种核酸底物的5‘羟基末端，通过测定不同长度和序列的单链(Ss)DNA寡核苷酸底物的一系列晶体结构来研究这一行为。在这些结构中，5‘核糖羟基以适当的排列方式埋藏在激酶活性部位，以进行磷酸转移。根据单链DNA的长度，前两个或三个核苷酸碱基是有序的。与磷核糖主链和有序碱基都进行了多次接触。5‘-GT DNA末端的有序碱基的位置、侧链接触和核苷酸间堆积作用与5’-TG末端的明显不同。PNK在这些位置显示的碱基偏好可归因于酶结合相互作用和每个独特底物分子的DNA构象的差异。
T4 phage polynucleotide kinase (PNK) displays 5'-hydroxyl kinase, 3'-phosphatase and 2',3'-cyclic phosphodiesterase activities. The enzyme phosphorylates the 5' hydroxyl termini of a wide variety of nucleic acid substrates, a behavior studied here through the determination of a series of crystal structures with single-stranded (ss)DNA oligonucleotide substrates of various lengths and sequences. In these structures, the 5' ribose hydroxyl is buried in the kinase active site in proper alignment for phosphoryl transfer. Depending on the ssDNA length, the first two or three nucleotide bases are well ordered. Numerous contacts are made both to the phosphoribosyl backbone and to the ordered bases. The position, side chain contacts and internucleotide stacking interactions of the ordered bases are strikingly different for a 5'-GT DNA end than for a 5'-TG end. The base preferences displayed at those positions by PNK are attributable to differences in the enzyme binding interactions and in the DNA conformation for each unique substrate molecule.