Bottomley Matthew J, Lo Surdo Paola, Di Giovine Paolo, Cirillo Agostino, Scarpelli Rita, Ferrigno Federica, Jones Philip, Neddermann Petra, De Francesco Raffaele, Steinkühler Christian, Gallinari Paola, Carfí Andrea
Istituto di Ricerche di Biologia Molecolare P. Angeletti, Merck Research Laboratories, Via Pontina Km 30.600, 00040 Pomezia (Roma), Italy.
J Biol Chem. 2008 Sep 26;283(39):26694-704. doi: 10.1074/jbc.M803514200. Epub 2008 Jul 8.
Histone deacetylases (HDACs) regulate chromatin status and gene expression, and their inhibition is of significant therapeutic interest. To date, no biological substrate for class IIa HDACs has been identified, and only low activity on acetylated lysines has been demonstrated. Here, we describe inhibitor-bound and inhibitor-free structures of the histone deacetylase-4 catalytic domain (HDAC4cd) and of an HDAC4cd active site mutant with enhanced enzymatic activity toward acetylated lysines. The structures presented, coupled with activity data, provide the molecular basis for the intrinsically low enzymatic activity of class IIa HDACs toward acetylated lysines and reveal active site features that may guide the design of class-specific inhibitors. In addition, these structures reveal a conformationally flexible structural zinc-binding domain conserved in all class IIa enzymes. Importantly, either the mutation of residues coordinating the structural zinc ion or the binding of a class IIa selective inhibitor prevented the association of HDAC4 with the N-CoR.HDAC3 repressor complex. Together, these data suggest a key role of the structural zinc-binding domain in the regulation of class IIa HDAC functions.
组蛋白去乙酰化酶（HDACs）调节染色质状态和基因表达，对其进行抑制具有重要的治疗意义。迄今为止，尚未鉴定出IIa类HDACs的生物学底物，仅证明其对乙酰化赖氨酸具有低活性。在此，我们描述了组蛋白去乙酰化酶-4催化结构域（HDAC4cd）以及对乙酰化赖氨酸具有增强酶活性的HDAC4cd活性位点突变体的抑制剂结合和无抑制剂结构。所呈现的结构与活性数据相结合，为IIa类HDACs对乙酰化赖氨酸固有的低酶活性提供了分子基础，并揭示了可能指导设计类特异性抑制剂的活性位点特征。此外，这些结构揭示了在所有IIa类酶中保守的构象灵活的结构锌结合结构域。重要的是，协调结构锌离子的残基突变或IIa类选择性抑制剂的结合均阻止了HDAC4与N-CoR.HDAC3阻遏复合物的缔合。总之，这些数据表明结构锌结合结构域在IIa类HDAC功能调节中起关键作用。
