Y家族DNA聚合酶DinB和聚合酶κ的空间位阻门控残基对于dNTP诱导的构象变化至关重要。
Steric gate residues of Y-family DNA polymerases DinB and pol kappa are crucial for dNTP-induced conformational change.
作者信息
Nevin Philip, Engen John R, Beuning Penny J
机构信息
Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
出版信息
DNA Repair (Amst). 2015 May;29:65-73. doi: 10.1016/j.dnarep.2015.01.012. Epub 2015 Feb 4.
Discrimination against ribonucleotides by DNA polymerases is critical to preserve DNA integrity. For many DNA polymerases, including those of the Y family, rNTP discrimination has been attributed to steric clashes between a residue near the active site, the steric gate, and the 2'-hydroxyl of the incoming rNTP. Here we used hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to probe the effects of the steric gate in the Y-family DNA polymerases Escherichia coli DinB and human DNA pol κ. Formation of a ternary complex with a G:dCTP base pair in the active site resulted in slower hydrogen exchange relative to a ternary complex with G:rCTP in the active site. The protection from exchange was localized to regions both distal and proximal to the active site, suggesting that DinB and DNA pol κ adopt different conformations depending on the sugar of the incoming nucleotide. In contrast, when the respective steric gate residues were mutated to alanine, the differences in HDX between the dNTP- and rNTP-bound ternary complexes were attenuated such that for DinB(F13A) and pol κ(Y112A), ternary complexes with either G:dCTP or G:rCTP base pairs had similar HDX profiles. Furthermore, the HDX in these ternary complexes resembled that of the rCTP-bound state rather than the dCTP-bound state of the wild-type enzymes. Primer extension assays confirmed that DinB(F13A) and pol κ(Y112A) do not discriminate against rNTPs to the same extent as the wild-type enzymes. Our observations indicate that the steric gate is crucial for rNTP discrimination because of its role in specifically promoting a dNTP-induced conformational change and that rNTP discrimination occurs in a relatively closed state of the polymerases.
DNA聚合酶对核糖核苷酸的识别对于维持DNA完整性至关重要。对于许多DNA聚合酶,包括Y家族的那些聚合酶,rNTP识别归因于活性位点附近的一个残基(空间位阻门)与进入的rNTP的2'-羟基之间的空间冲突。在这里,我们使用氢/氘交换(HDX)质谱(MS)来探究Y家族DNA聚合酶大肠杆菌DinB和人类DNA聚合酶κ中空间位阻门的作用。与活性位点中G:dCTP碱基对形成三元复合物导致相对于活性位点中G:rCTP的三元复合物,氢交换较慢。免受交换的保护作用定位于活性位点远端和近端的区域,这表明DinB和DNA聚合酶κ根据进入核苷酸的糖采取不同的构象。相比之下,当各自的空间位阻门残基突变为丙氨酸时,dNTP结合和rNTP结合的三元复合物之间的HDX差异减弱,以至于对于DinB(F13A)和聚合酶κ(Y112A),具有G:dCTP或G:rCTP碱基对的三元复合物具有相似的HDX谱。此外,这些三元复合物中的HDX类似于野生型酶的rCTP结合状态而不是dCTP结合状态。引物延伸试验证实DinB(F13A)和聚合酶κ(Y112A)对rNTPs的识别程度与野生型酶不同。我们的观察结果表明,空间位阻门对于rNTP识别至关重要,因为它在特异性促进dNTP诱导的构象变化中起作用,并且rNTP识别发生在聚合酶相对封闭的状态下。