改变 dNTP 离去基团的碱性可调节 DNA 聚合酶 β 的前催化构象变化。

IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Khadijeh S. Alnajjar, Katarina Wang, Isabel Alvarado-Cruz, Cristian Chavira, Amirsoheil Negahbani, Maryam Nakhjiri, Corinne Minard, Beatriz Garcia-Barboza, Boris A. Kashemirov, Charles E. McKenna, Myron F. Goodman and Joann B. Sweasy*, 
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引用次数: 0

摘要

DNA 聚合酶 β(pol β)的催化功能是将单个核苷酸整合到因移除受损 DNA 碱基而产生间隙的 DNA 底物中,从而满足碱基切除 DNA 修复途径的间隙填充要求。最重要的是,Pol β 可以从结构相似的核苷酸池中选择正确的核苷酸,将其整合到 DNA 中,以防止基因组中突变的积累。Pol β可能采用了多种底物选择机制。在这里,我们使用在三磷酸分子的β,γ桥接基团上经过修饰的 dCTP 类似物来监测输入核苷酸的离去基团碱性对催化前构象变化的影响,这种变化对催化作用和选择性非常重要。以前的研究表明,离去基团 pKa 与化学转变状态之间存在线性自由能关系。我们的研究结果表明,前催化构象变化(特别是 pol β 的手指亚域的关闭)的速率也有类似的关系。此外,通过利用类似的 β,γ-CHX 立体异构体,我们发现 β,γ-桥接基团相对于 R183 的取向对手指关闭的速率很重要,这直接影响了化学反应。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β

Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β

Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β

The catalytic function of DNA polymerase β (pol β) fulfills the gap-filling requirement of the base excision DNA repair pathway by incorporating a single nucleotide into a gapped DNA substrate resulting from the removal of damaged DNA bases. Most importantly, pol β can select the correct nucleotide from a pool of similarly structured nucleotides to incorporate into DNA in order to prevent the accumulation of mutations in the genome. Pol β is likely to employ various mechanisms for substrate selection. Here, we use dCTP analogues that have been modified at the β,γ-bridging group of the triphosphate moiety to monitor the effect of leaving group basicity of the incoming nucleotide on precatalytic conformational changes, which are important for catalysis and selectivity. It has been previously shown that there is a linear free energy relationship between leaving group pKa and the chemical transition state. Our results indicate that there is a similar relationship with the rate of a precatalytic conformational change, specifically, the closing of the fingers subdomain of pol β. In addition, by utilizing analogue β,γ-CHX stereoisomers, we identified that the orientation of the β,γ-bridging group relative to R183 is important for the rate of fingers closing, which directly influences chemistry.

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来源期刊
Biochemistry Biochemistry
Biochemistry Biochemistry 生物-生化与分子生物学
CiteScore
5.50
自引率
3.40%
发文量
336
审稿时长
1-2 weeks
期刊介绍: Biochemistry provides an international forum for publishing exceptional, rigorous, high-impact research across all of biological chemistry. This broad scope includes studies on the chemical, physical, mechanistic, and/or structural basis of biological or cell function, and encompasses the fields of chemical biology, synthetic biology, disease biology, cell biology, nucleic acid biology, neuroscience, structural biology, and biophysics. In addition to traditional Research Articles, Biochemistry also publishes Communications, Viewpoints, and Perspectives, as well as From the Bench articles that report new methods of particular interest to the biological chemistry community.
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