Structure and Function of JmjC Histone Demethylases

JmjC 组蛋白去甲基酶的结构和功能

• 批准号: 7247686
• 负责人: GONGYI ZHANG
• 金额: $ 29.64万
• 依托单位: NATIONAL JEWISH HEALTH
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7247686
• 关键词: Acetylation; Address; Binding; Binding Sites; Biochemical Reaction; Biological Assay; Biological Process; C-terminal; Catalytic Domain; Characteristics; Chromatin Structure; Complex; Core Protein; Deacetylation; Elements; Epigenetic Process; Eukaryotic Cell; Family; Family member; Gene Expression Regulation; Genes; Genomic Imprinting; Goals; Half-Life; Heme; Heterochromatin; Histones; Homeobox Genes; Homologous Gene; Laboratories; Link; Lysine; Malignant Neoplasms; Methylation; Modification; Mono-S; Mutagenesis; Mutate; N Domain; Nuclear; Numbers; Other Finding; Oxygenases; Peptides; Plants; Process; Protein Family; Proteins; Research Personnel; Resolution; Role; Specificity; Structure; Substrate Specificity; Variant; Work; X Inactivation; Zinc Fingers; amine oxidase; base; cofactor; demethylation; enzyme activity; experience; homeodomain; human disease; member; methyl group; novel; programs; protein structure; protein structure function

DESCRIPTION (provided by applicant): Covalent modifications of histone proteins, essential regulators of the activity of genes in eukaryotic cells, remodel the chromatin structure via a variety of enzymatic reactions. The reversible processes of some modifications, such as acetylation and deacetylation, are well characterized. Whether methylation and demethylation reversibly contribute to gene regulation, however, remains controversial. Recent studies have shown that methylation and demethylation are universally used to posttranslationally modify histones for the regulation of gene activity. In addition to LSD1, a nuclear amine oxidase homolog, which was found to function as a histone lysine demethylase, we and others found that some JmjC domain-containing proteins are histone demethylases. Specifically, we found that members of the JMJD2 protein family are histone demethylases that act on trimethyl groups of H3-K9 and H3-K36. Moreover, some members of this family also have activity for dimethyl groups. To understand the relationships between the structures and functions of these proteins, we have determined the structure of the catalytic core of the JMJD2A protein. From this structure, several novel structure features were revealed, such as the novel JmjN domain, the JmjC domain, the C-terminal domain, and a zinc finger motif. These unique structural features create a potential catalytic center. The structure also revealed a characteristic signature motif, which includes structural determinants for cofactors such as Fe(II) and a-ketoglutarate, a hallmark of non-heme containing oxygenases. There, however, are major questions that remained to be answered, such as the structural basis of the recognition of the substrate peptides by the catalytic core, the structural determinants of the specificity for the methyl groups, the mechanisms that regulate the activity of the enzyme, and the relationships among different JmjC domain-containing histone demethylases. Furthermore, only a small percentage of JmjC domain-containing proteins have been characterized. We believe that there are uncharacterized histone demethylases within the family of JmjC domain-containing proteins. Structural information derived from JMJD2A should be helpful in revealing these new histone demethylases. To answer these questions and to understand how the JmjC domain-containing histone demethylases function, three specific aims are proposed. Specific aim 1 - To characterize the structures and functions of the JMJD2 family members and to identify new histone demethylases; Specific aim 2 - To determine the high-resolution structures of the catalytic core of JMJD2A in the presence of different substrate peptides; Specific aim 3 - To determine the high-resolution structures of the entire JMJD2A protein and of the catalytic cores of other JmjC domain-containing proteins and to reveal the mechanisms that regulate the activity of JMJD2A and other related proteins.

描述（由申请人提供）：组蛋白的共价修饰是真核细胞中基因活性的重要调节剂，通过各种酶促反应重塑染色质结构。一些修饰的可逆过程，例如乙酰化和脱乙酰化，已得到很好的表征。然而，甲基化和去甲基化是否可逆地促进基因调控仍然存在争议。最近的研究表明，甲基化和去甲基化普遍用于翻译后修饰组蛋白以调节基因活性。除了LSD1（一种核胺氧化酶同源物，被发现具有组蛋白赖氨酸去甲基化酶功能）之外，我们和其他人还发现一些含有JmjC结构域的蛋白质是组蛋白去甲基化酶。具体来说，我们发现 JMJD2 蛋白家族的成员是作用于 H3-K9 和 H3-K36 三甲基的组蛋白去甲基酶。此外，该家族的一些成员还具有二甲基活性。为了了解这些蛋白质的结构和功能之间的关系，我们确定了 JMJD2A 蛋白质催化核心的结构。从该结构中，揭示了一些新颖的结构特征，例如新颖的 JmjN 结构域、JmjC 结构域、C 末端结构域和锌指基序。这些独特的结构特征创造了潜在的催化中心。该结构还揭示了一个特征性的特征基序，其中包括辅助因子的结构决定因素，例如 Fe(II) 和 α-酮戊二酸，这是不含血红素的加氧酶的标志。然而，仍有一些主要问题有待解答，例如催化核心识别底物肽的结构基础、甲基特异性的结构决定因素、调节酶活性的机制，以及不同含 JmjC 结构域的组蛋白去甲基酶之间的关系。此外，仅对一小部分含有 JmjC 结构域的蛋白质进行了表征。我们认为含有 JmjC 结构域的蛋白质家族中存在未表征的组蛋白去甲基酶。来自 JMJD2A 的结构信息应该有助于揭示这些新的组蛋白去甲基化酶。为了回答这些问题并了解包含 JmjC 结构域的组蛋白去甲基酶如何发挥作用，提出了三个具体目标。具体目标 1 - 表征 JMJD2 家族成员的结构和功能并鉴定新的组蛋白去甲基酶；具体目标2 - 确定JMJD2A催化核心在不同底物肽存在下的高分辨率结构；具体目标 3 - 确定整个 JMJD2A 蛋白和其他含 JmjC 结构域蛋白的催化核心的高分辨率结构，并揭示调节 JMJD2A 和其他相关蛋白活性的机制。