Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate.
Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate.
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DOI：
10.1371/journal.pone.0131507
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Nordlund P
中科院分区：
文献类型：
--
作者：
Trésaugues L;Lundbäck T;Welin M;Flodin S;Nyman T;Silvander C;Gräslund S;Nordlund P
人NUDT 16是NUDIX水解酶超家族的成员。在最初被描述为mRNA脱帽酶之后，最近的研究赋予它作为“大扫除”酶的作用，专门用于从核苷酸库中去除有害的（脱氧）肌苷二磷酸。在这里，我们提出了人NUDT 16的晶体结构，无论是在其apo形式和与其产品肌苷一磷酸（IMP）的复合物。NUDT 16表现为二聚体，其形成产生带正电荷的沟槽以适应底物结合。详细的酶和生物物理研究的结构数据的补充揭示了底物识别的决定因素，特别是嘌呤环上位置2和6的取代基的重要性。IMP产品的亲和力，窝藏羰基在6位的基础上，相比嘌呤单磷酸缺乏H-键受体在这个位置上，意味着一个催化循环，其速率主要是由产品释放步骤调节。最后，我们还表征了反应产物IMP的抑制现象，其可能排除NUDT 16介导的水解的无害核苷酸，而不管它们的细胞浓度如何。总之，本研究详细说明了结构和调节机制，解释了如何选择底物进行人NUDT 16水解。
Human NUDT16 is a member of the NUDIX hydrolase superfamily. After having been initially described as an mRNA decapping enzyme, recent studies conferred it a role as an “housecleaning” enzyme specialized in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. Here we present the crystal structure of human NUDT16 both in its apo-form and in complex with its product inosine monophosphate (IMP). NUDT16 appears as a dimer whose formation generates a positively charged trench to accommodate substrate-binding. Complementation of the structural data with detailed enzymatic and biophysical studies revealed the determinants of substrate recognition and particularly the importance of the substituents in position 2 and 6 on the purine ring. The affinity for the IMP product, harboring a carbonyl in position 6 on the base, compared to purine monophosphates lacking a H-bond acceptor in this position, implies a catalytic cycle whose rate is primarily regulated by the product-release step. Finally, we have also characterized a phenomenon of inhibition by the product of the reaction, IMP, which might exclude non-deleterious nucleotides from NUDT16-mediated hydrolysis regardless of their cellular concentration. Taken together, this study details structural and regulatory mechanisms explaining how substrates are selected for hydrolysis by human NUDT16.
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DOI：
10.1107/s0907444905036693
发表时间：
2006-01-01
影响因子：
2.2
作者：
Evans, P
通讯作者：
Evans, P
影响因子：
5.8
作者：
Gouet, P;Courcelle, E;Métoz, F
通讯作者：
Métoz, F
DOI：
10.1073/pnas.131009198
发表时间：
2001-07-17
影响因子：
11.1
作者：
Kuzminov, A
通讯作者：
Kuzminov, A
影响因子：
4.9
作者：
Munoz, Francisco Jose;Baroja-Fernandez, Edurne;Pozueta-Romero, Javier
通讯作者：
Pozueta-Romero, Javier
影响因子：
21.1
作者：
Lu, Guangwen;Zhang, Jie;Yan, Jinghua
通讯作者：
Yan, Jinghua