Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States.
Biochemistry. 2019 Dec 10;58(49):4912-4924. doi: 10.1021/acs.biochem.9b00934. Epub 2019 Dec 2.
Histone deacetylase 6 (HDAC6) is emerging as a target for inhibition in therapeutic strategies aimed at treating cancer, neurodegenerative disease, and other disorders. Among the metal-dependent HDAC isozymes, HDAC6 is unique in that it contains two catalytic domains, CD1 and CD2. CD2 is a tubulin deacetylase and a tau deacetylase, and the development of HDAC6-selective inhibitors has focused exclusively on this domain. In contrast, there is a dearth of structural and functional information regarding CD1, which exhibits much narrower substrate specificity in comparison with CD2. As the first step in addressing the CD1 information gap, we now present X-ray crystal structures of seven inhibitor complexes with wild-type, Y363F, and K330L HDAC6 CD1. These structures broaden our understanding of molecular features that are important for catalysis and inhibitor binding. The active site of HDAC6 CD1 is wider than that of CD2, which is unexpected in view of the narrow substrate specificity of CD1. Amino acid substitutions between HDAC6 CD1 and CD2, as well as conformational differences in conserved residues, define striking differences in active site contours. Catalytic activity measurements with HDAC6 CD1 confirm the preference for peptide substrates containing C-terminal acetyllysine residues. However, these measurements also show that CD1 exhibits weak activity for peptide substrates bearing certain small amino acids on the carboxyl side of the scissile acetyllysine residue. Taken together, these results establish a foundation for understanding the structural basis of HDAC6 CD1 catalysis and inhibition, pointing to possible avenues for the development of HDAC6 CD1-selective inhibitors.
组蛋白去乙酰化酶 6（HDAC6）作为治疗癌症、神经退行性疾病和其他疾病的治疗策略的抑制靶点而备受关注。在金属依赖性 HDAC 同工酶中，HDAC6 是独特的，因为它包含两个催化结构域，CD1 和 CD2。CD2 是微管蛋白脱乙酰酶和tau 脱乙酰酶，HDAC6 选择性抑制剂的开发完全集中在这个结构域上。相比之下，CD1 的结构和功能信息匮乏，与 CD2 相比，其底物特异性要窄得多。作为解决 CD1 信息缺口的第一步，我们现在展示了与野生型、Y363F 和 K330L HDAC6 CD1 结合的七个抑制剂复合物的 X 射线晶体结构。这些结构拓宽了我们对对于催化和抑制剂结合很重要的分子特征的理解。HDAC6 CD1 的活性位点比 CD2 宽，这与 CD1 的窄底物特异性不符。HDAC6 CD1 和 CD2 之间的氨基酸取代以及保守残基的构象差异，定义了活性位点轮廓的显著差异。使用 HDAC6 CD1 进行的催化活性测量证实了对含有 C 末端乙酰赖氨酸残基的肽底物的偏好。然而，这些测量还表明，CD1 对带有某些小氨基酸的裂解乙酰赖氨酸残基羧基侧的肽底物表现出较弱的活性。总之，这些结果为理解 HDAC6 CD1 催化和抑制的结构基础奠定了基础，并指出了开发 HDAC6 CD1 选择性抑制剂的可能途径。
