Deng Wen-Hao, Lewin Harry, Liao Rong-Zhen, Rosta Edina
Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China.
Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom.
ACS Catal. 2025 Jun 1;15(12):10176-10187. doi: 10.1021/acscatal.5c01682. eCollection 2025 Jun 20.
2'-Deoxynucleoside-5'-triphosphate triphosphohydrolases (dNTPases) constitute a crucial enzyme family that plays a pivotal role in antiviral innate immunity. Among these enzymes, human SAMHD1 has emerged as a dNTPase with distinct catalytic properties and active-site architecture. This metalloenzyme regulates cellular dNTP concentration through its ability to hydrolyze all four canonical dNTPs into their corresponding 2'-deoxynucleosides and inorganic triphosphates, a reaction requiring coordinated iron and magnesium ions for enzymatic activity. In the present work, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to investigate the mechanistic details of dATP hydrolysis mediated by two metal ions. Starting from the resolved crystal structure, Model-1, containing a Fe in the active site, was constructed. Our calculations demonstrate that SAMHD1 employs a bridging hydroxide anion OH to attack the Pα site of dNTP, triggering the cleavage of the Pα-O5' bond via a trigonal-bipyramidal transition state. Simultaneously, His215 donates a proton to O5' of the leaving group, leading to the formation of 2'-deoxyadenosine and triphosphate ion. It is further demonstrated that the native Fe-Mg bimetallic center help catalyze this hydrolysis reaction with a barrier of 13.4 kcal/mol, while the substitution from Fe to Fe abolishes the catalytic activity of SAMHD1. The comparison between different QM/MM models highlight the high affinity of SAMHD1 for Fe relative to Mn and Mg at one of the bimetallic sites. In addition, the metal ion swapping between Fe and Mg from their crystallographic positions is shown to elevate the energy of the reactant state, underscoring the critical influence of the metal coordination geometry on catalytic activity. These computational insights not only expand the understanding of how SAMHD1 wisely modulates catalytic reactivity and metal selectivity by binding suitable metal ions but also provide a valuable foundation for guiding the design of drugs for antiviral therapies.
2'-脱氧核苷-5'-三磷酸三磷酸水解酶（dNTPases）构成了一个关键的酶家族，在抗病毒先天免疫中发挥着核心作用。在这些酶中，人类SAMHD1已成为一种具有独特催化特性和活性位点结构的dNTPase。这种金属酶通过将所有四种典型的dNTP水解为相应的2'-脱氧核苷和无机三磷酸，来调节细胞内dNTP的浓度，该反应需要铁离子和镁离子协同作用以实现酶活性。在本研究中，采用分子动力学（MD）模拟和量子力学/分子力学（QM/MM）计算来研究由两种金属离子介导的dATP水解的机制细节。从解析的晶体结构出发，构建了活性位点含有铁的模型1。我们的计算表明，SAMHD1利用一个桥连的氢氧根阴离子OH攻击dNTP的Pα位点，通过三角双锥过渡态引发Pα-O5'键的断裂。同时，His215将一个质子捐赠给离去基团的O5'，导致2'-脱氧腺苷和三磷酸离子的形成。进一步证明，天然的铁-镁双金属中心有助于催化该水解反应，其能垒为13.4千卡/摩尔，而将铁替换为锰则消除了SAMHD1的催化活性。不同QM/MM模型之间的比较突出了SAMHD1在双金属位点之一对铁相对于锰和镁的高亲和力。此外，铁和镁在其晶体学位置之间的金属离子交换显示会提高反应物状态的能量，强调了金属配位几何结构对催化活性的关键影响。这些计算见解不仅扩展了我们对SAMHD1如何通过结合合适的金属离子明智地调节催化反应性和金属选择性的理解，还为指导抗病毒治疗药物的设计提供了有价值的基础。
