Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state.
Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state.
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DOI：
10.1038/s41467-022-34752-1
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发表时间：
2022-11-19
影响因子：
16.6
通讯作者：
Matsuo, Hiroshi
中科院分区：
文献类型：
--
作者：
Maiti, Atanu;Hedger, Adam K.;Myint, Wazo;Balachandran, Vanivilasini;Watts, Jonathan K.;Schiffer, Celia A.;Matsuo, Hiroshi
APOBEC 3蛋白（A3）是催化单链DNA（ssDNA）底物中胞苷脱氨基为尿苷的酶，因此在先天性抗病毒免疫中起关键作用。然而，APOBEC 3家族也与癌细胞中的许多突变特征有关，这导致人们对开发A3催化活性的抑制剂作为治疗剂以及研究A3生物化学，结构和细胞功能的工具产生了浓厚的兴趣。最近的研究表明，含有2′-脱氧-zebularine（dZ-ssDNA）的ssDNA是A3 s如A3 A，A3 B和A3 G的抑制剂，尽管这种活性的原子决定因素仍然未知。为了填补这一知识空白，我们确定了与活性A3 G结合的dZ-ssDNA抑制剂的1.5 μ m分辨率结构。晶体结构显示，活化的dZ-H2O通过与活性位点Zn 2+配位并参与额外的稳定相互作用（例如与催化残基E259的相互作用）来模拟过渡态。因此，这种结构使我们能够捕获A3过渡态的快照，并表明开发过渡态模拟抑制剂可能为未来设计更多针对A3的分子提供新的机会。在这里，APOBEC 3G的酶活性导致2 '-脱氧-zebularine转化为水合产物，使作者能够捕获过渡态，这为设计此类酶的新型过渡态模拟抑制剂提供了蓝图。
APOBEC3 proteins (A3s) are enzymes that catalyze the deamination of cytidine to uridine in single-stranded DNA (ssDNA) substrates, thus playing a key role in innate antiviral immunity. However, the APOBEC3 family has also been linked to many mutational signatures in cancer cells, which has led to an intense interest to develop inhibitors of A3’s catalytic activity as therapeutics as well as tools to study A3’s biochemistry, structure, and cellular function. Recent studies have shown that ssDNA containing 2′-deoxy-zebularine (dZ-ssDNA) is an inhibitor of A3s such as A3A, A3B, and A3G, although the atomic determinants of this activity have remained unknown. To fill this knowledge gap, we determined a 1.5 Å resolution structure of a dZ-ssDNA inhibitor bound to active A3G. The crystal structure revealed that the activated dZ-H2O mimics the transition state by coordinating the active site Zn2+ and engaging in additional stabilizing interactions, such as the one with the catalytic residue E259. Therefore, this structure allowed us to capture a snapshot of the A3’s transition state and suggests that developing transition-state mimicking inhibitors may provide a new opportunity to design more targeted molecules for A3s in the future. Here, the enzymatic activity of APOBEC3G resulting in conversion of 2′-deoxy-zebularine into a hydration product allowed the authors to capture the transition state, which provides a blueprint for designing a new class of transition state-mimicking inhibitors for this class of enzyme.
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DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
7.3
作者：
DORSEY, BD;LEVIN, RB;HUFF, JR
通讯作者：
HUFF, JR
DOI：
10.1107/s0907444909042073
发表时间：
2010-01
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Chen VB;Arendall WB 3rd;Headd JJ;Keedy DA;Immormino RM;Kapral GJ;Murray LW;Richardson JS;Richardson DC
通讯作者：
Richardson DC
影响因子：
8
作者：
Cannataro, Vincent L.;Gaffney, Stephen G.;Townsend, Jeffrey P.
通讯作者：
Townsend, Jeffrey P.
影响因子：
4.9
作者：
De Meyer, S;Azijn, H;de Béthune, MP
通讯作者：
de Béthune, MP