Silvestrov Pavel, Müller Tina A, Clark Kristen N, Hausinger Robert P, Cisneros G Andrés
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States.
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States.
J Mol Graph Model. 2014 Nov;54:123-30. doi: 10.1016/j.jmgm.2014.10.013. Epub 2014 Oct 27.
The ability to repair DNA is important for the conservation of genetic information of living organisms. Cells have a number of ways to restore damaged DNA, such as direct DNA repair, base excision repair, and nucleotide excision repair. One of the proteins that can perform direct repair of DNA bases is Escherichia coli AlkB. In humans, there are 9 identified AlkB homologs, including AlkB homolog 1 (ALKBH1). Many of these proteins catalyze the direct oxidative dealkylation of DNA and RNA bases and, as such, have an important role in repairing DNA from damage induced by alkylating agents. In addition to the dealkylase activity, ALKBH1 can also function as an apyrimidinic/apurinic lyase and was proposed to have a distinct lyase active site. To our knowledge, no crystal structure or complete homology model of ALKBH1 protein is available. In this study, we have used homology modeling to predict the structure of ALKBH1 based on AlkB and Duffy-binding-like domain crystal structures as templates. Molecular dynamics simulations were subsequently performed on the predicted structure of ALKBH1. The positions of two disulfide bonds or a zinc-finger motif and a disulfide bond were predicted and the importance of these features was tested by mutagenesis. Possible locations for the lyase active site are proposed based on the analysis of our predicted structures and previous experimental results.
修复DNA的能力对于保存生物体的遗传信息至关重要。细胞有多种修复受损DNA的方式，如直接DNA修复、碱基切除修复和核苷酸切除修复。能够对DNA碱基进行直接修复的蛋白质之一是大肠杆菌AlkB。在人类中，已鉴定出9种AlkB同源物，包括AlkB同源物1（ALKBH1）。这些蛋白质中的许多都催化DNA和RNA碱基的直接氧化脱烷基化反应，因此在修复由烷基化剂诱导的DNA损伤中发挥重要作用。除了脱烷基酶活性外，ALKBH1还可作为脱嘧啶/脱嘌呤裂解酶发挥作用，并被认为具有独特的裂解酶活性位点。据我们所知，目前尚无ALKBH1蛋白的晶体结构或完整的同源模型。在本研究中，我们以AlkB和达菲结合样结构域晶体结构为模板，利用同源建模预测了ALKBH1的结构。随后对预测的ALKBH1结构进行了分子动力学模拟。预测了两个二硫键或一个锌指基序和一个二硫键的位置，并通过诱变测试了这些特征的重要性。基于对我们预测结构的分析和先前的实验结果，提出了裂解酶活性位点的可能位置。
