Structures of human sirtuin 3 complexes with ADP-ribose and with carba-NAD+ and SRT1720: binding details and inhibition mechanism
Structures of human sirtuin 3 complexes with ADP-ribose and with carba-NAD+ and SRT1720: binding details and inhibition mechanism
复制标题
DOI：
10.1107/s0907444913015448
复制
发表时间：
2013-08-01
影响因子：
2.2
通讯作者：
Steegborn, Clemens
中科院分区：
文献类型：
--
作者：
Giang Thi Tuyet Nguyen;Schaefer, Susanne;Steegborn, Clemens
Sirtuins 是 NAD(+) 依赖性蛋白脱乙酰酶，可调节代谢和衰老过程，被认为是有吸引力的治疗靶点。大多数可用的沉默调节蛋白调节剂在机制上知之甚少，这阻碍了它们的改进。 SRT1720 最初被描述为人类 Sirt1 的激活剂，但它也能有效抑制人类 Sirt3。在此，描述了 SRT1720 抑制 Sirt3 的分子机制。 Sirt3 与 SRT1720 和 NAD(+) 类似物复合的晶体结构表明，该化合物部分占据乙酰基-赖氨酸结合位点，从而解释了所报道的与肽底物的竞争。该化合物包裹在疏水性蛋白质片上，并通过其相对表面与 NAD(+) 烟酰胺结合，从而产生异常紧密的三明治状相互作用。观察到的排列合理化了 NAD(+) 的非竞争性抑制，并且结合测量证实了 NAD(+) 的烟酰胺部分支持抑制剂结合。一致地，Sirt3 的第二个晶体结构中没有结合任何抑制剂，该结构与 ADP-核糖复合溶解并在 SRT1720 存在下结晶。这些结果揭示了一个新的sirtuin抑制剂结合位点和机制，并为化合物的改进提供了结构基础。
Sirtuins are NAD(+)-dependent protein deacetylases that regulate metabolism and aging processes and are considered to be attractive therapeutic targets. Most available sirtuin modulators are little understood mechanistically, hindering their improvement. SRT1720 was initially described as an activator of human Sirt1, but it also potently inhibits human Sirt3. Here, the molecular mechanism of the inhibition of Sirt3 by SRT1720 is described. A crystal structure of Sirt3 in complex with SRT1720 and an NAD(+) analogue reveals that the compound partially occupies the acetyl-Lys binding site, thus explaining the reported competition with the peptide substrate. The compound packs against a hydrophobic protein patch and binds with its opposite surface to the NAD(+) nicotinamide, resulting in an exceptionally tight sandwich-like interaction. The observed arrangement rationalizes the uncompetitive inhibition with NAD(+), and binding measurements confirm that the nicotinamide moiety of NAD(+) supports inhibitor binding. Consistently, no inhibitor is bound in a second crystal structure of Sirt3 that was solved complexed with ADP-ribose and crystallized in the presence of SRT1720. These results reveal a novel sirtuin inhibitor binding site and mechanism, and provide a structural basis for compound improvement.