组蛋白甲基转移酶

组蛋白甲基转移酶（英語：Histone methyltransferase，简称为HMT）是包括组蛋白-赖氨酸N-甲基转移酶与组蛋白-精氨酸N-甲基转移酶在内的是一大類组蛋白修饰酶类，它们催化将一个、两个或三个甲基转移到组蛋白的赖氨酸或精氨酸残基上。被添加上的甲基基团主要位于组蛋白H3和H4的特定赖氨酸或精氨酸上^[1]。

组蛋白-赖氨酸 N-甲基转移酶
命名 系统命名 缩写
识别码
EC編號	2.1.1.43
CAS号	9055-08-7
数据库
IntEnz	IntEnz浏览
BRENDA（英语：BRENDA）	BRENDA入口
ExPASy（英语：ExPASy）	NiceZyme浏览
KEGG	KEGG入口
MetaCyc（英语：MetaCyc）	代谢路径
PRIAM（英语：PRIAM_enzyme-specific_profiles）	概述
PDB	RCSB PDB PDBj PDBe PDBsum
基因本体	AmiGO / EGO
搜索 PMC 相关文献 PubMed 相关文献

种类

赖氨酸特异性组蛋白甲基转移酶类可被细分为含SET结构域的和不含SET结构域的两类。顾名思义，它们之间的区别在于存不存在SET这样一种结构域。

人类基因所编码的具有组蛋白甲基转移酶活性的蛋白质包括：

• ASH1L
• DOT1L
• EHMT1、EHMT2、EZH1、EZH2
• MLL、MLL2、MLL3、MLL4、MLL5
• NSD1
• PRDM2
• SET、SETBP1、SETD1A、SETD1B、SETD2、SETD3、SETD4、SETD5、SETD6、SETD7、SETD8、SETD9、SETDB1、SETDB2
• SETMAR、SMYD1、SMYD2、SMYD3、SMYD4、SMYD5、SUV39H1、SUV39H2、SUV420H1、SUV420H2

含SET结构域的赖氨酸特异性组蛋白甲基转移酶

结构

影响甲基转移酶活性的结构包括：SET结构域（包括130个氨基酸）、前SET和后SET结构域。前SET区域包括半胱氨酸残基，可形成三角锌簇，紧密结合锌原子并使结构稳定。SET结构域本身包含一个富含β-股的催化核心，从而形成几个β折叠区域。 一般在前SET结构域发现的β-股将形成的β-折叠，它带有SET结构域的β-股，导致SET结构域结构的细微变化。

These small changes alter the target residue site specificity for methylation and allow the SET domain methyltransferases to target many different residues. This interplay between the pre-SET domain and the catalytic core is critical for enzyme function.^[1]

催化机制

In order for the reaction to proceed, S-Adenosyl methionine (SAM) and the lysine residue of the substrate histone tail must first be bound and properly oriented in the catalytic pocket of the SET domain. Next, a nearby tyrosine residue deprotonates the ε-amino group of the lysine residue.^[2] The lysine chain then makes a nucleophilic attack on the methyl group on the sulfur atom of the SAM molecule, transferring the methyl group to the lysine side chain.

 

Active site of Histone Lysine N-Methyltransferase. Lysine residue (in yellow) and S-Adenosyl methionine (SAM) (in blue) clearly visible.

不含SET结构域的赖氨酸特异性组蛋白甲基转移酶

Instead of SET, non-SET domain-containing histone methyltransferase utilizes the enzyme Dot1. Unlike the SET domain, which targets the lysine tail region of the histone, Dot1 methylates a lysine residue in the globular core of the histone, and is the only enzyme known to do so.^[1] A possible homolog of Dot1 was found in archaea which shows the ability to methylate archaeal histone-like protein in recent studies.

结构

The N terminal of Dot1 contains the active site. A loop serving as the binding site for SAM links the N-terminal and the C-terminal domains of the Dot1 catalytic domain. The C-terminal is important for the substrate specificity and binding of Dot1 because the region carries a positive charge, allowing for a favorable interaction with the negatively charged backbone of DNA.^[3] Due to structural constraints, Dot1 is only able to methylate histone H3.

精氨酸特异性组蛋白甲基转移酶

There are two different types of protein arginine methyltransferases (PRMTs) and three types of methylation that can occur at arginine residues on histone tails. The first type of PRMTs (PRMT1, PRMT3, CARM1⧸PRMT4, and Rmt1⧸Hmt1) produce monomethylarginine and asymmetric dimethylarginine.^[4][5][6] The second type (JBP1⧸PRMT5) produces monomethyl or symmetric dimethylarginine.^[7] The differences in the two types of PRMTs arise from restrictions in the arginine binding pocket.^[7]

结构

The catalytic domain of PRMTs consists of a SAM binding domain and substrate binding domain (about 310 amino acids in total).^[7][8][9] Each PRMT has a unique N-terminal region and a catalytic core. The arginine residue and SAM must be correctly oriented within the binding pocket. SAM is secured inside the pocket by a hydrophobic interaction between an adenine ring and a phenyl ring of a phenylalanine.^[9]

催化机制

A glutamate on a nearby loop interacts with nitrogens on the target arginine residue. This interaction redistributes the positive charge and leads to the deprotonation of one nitrogen group,^[10] which can then make a nucleophilic attack on the methyl group of SAM. Differences between the two types of PRMTs determine the next methylation step: either catalyzing the dimethylation of one nitrogen or allowing the symmetric methylation of both groups.^[7] However, in both cases the proton stripped from the nitrogen is dispersed through a histidine–aspartate proton relay system and released into the surrounding matrix.^[11]

在基因调控中的作用

Histone methylation plays an important role in epigenetic gene regulation. Methylated histones can either repress or activate transcription as different experimental findings suggest. For example, it is likely that the methylation of lysine 9 on histone H3 (H3K9me3) in the promoter region of genes prevents excessive expression of these genes and, therefore, delays cell cycle transition and/or proliferation.^[12] See Histone#Chromatin regulation.

疾病的相关性

Abnormal expression or activity of methylation-regulating enzymes has been noted in some types of human cancers, suggesting associations between histone methylation and malignant transformation of cells or formation of tumors.^[12] In recent years, epigenetic modification of the histone proteins, especially the methylation of the histone H3, in cancer development has been an area of emerging research. It is now generally accepted that in addition to genetic aberrations, cancer can be initiated by epigenetic changes in which gene expression is altered without genomic abnormalities. These epigenetic changes include loss or gain of methylations in both DNA and histone proteins.^[12]

There is not yet compelling evidence that suggests cancers develop purely by abnormalities in histone methylation or its signaling pathways, however they may be a contributing factor. For example, down-regulation of methylation of lysine 9 on histone 3 (H3K9me3) has been observed in several types of human cancer (such as colorectal cancer, ovarian cancer, and lung cancer), which arise from either the deficiency of H3K9 methyltransferases or elevated activity or expression of H3K9 demethylases.^[12][13][14]

进一步研究

组蛋白甲基转移酶可以用作癌症的诊断和预后的生物标志物。 另外，关于组蛋白甲基转移酶在细胞的恶性转化，组织的癌发生和肿瘤发生中的功能和调节仍然存在许多问题^[12]。

另见

• 组蛋白修饰酶类（英语：Histone-modifying enzymes）
• 组蛋白乙酰转移酶（HAT）
• 组蛋白脱乙酰酶（HDAC）
• 组蛋白甲基化
• 核小體
• 染色质

参考文献

1. Wood A. Posttranslational Modifications of Histones by Methylation. Conaway JW, Conaway RC (编). Proteins in eukaryotic transcription. Advances in Protein Chemistry 67. Amsterdam: Elsevier Academic Press. 2004: 201–222. ISBN 0-12-034267-7. doi:10.1016/S0065-3233(04)67008-2. 
2. Trievel RC, Beach BM, Dirk LM, Houtz RL, Hurley JH. Structure and catalytic mechanism of a SET domain protein methyltransferase. Cell. October 2002, 111 (1): 91–103. PMID 12372303. doi:10.1016/S0092-8674(02)01000-0. 
3. Min J, Feng Q, Li Z, Zhang Y, Xu RM. Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell. March 2003, 112 (5): 711–23. PMID 12628190. doi:10.1016/S0092-8674(03)00114-4. 
4. Chen D, Ma H, Hong H, Koh SS, Huang SM, Schurter BT, Aswad DW, Stallcup MR. Regulation of transcription by a protein methyltransferase. Science. June 1999, 284 (5423): 2174–7. PMID 10381882. doi:10.1126/science.284.5423.2174. 
5. Gary JD, Lin WJ, Yang MC, Herschman HR, Clarke S. The predominant protein-arginine methyltransferase from Saccharomyces cerevisiae. J. Biol. Chem. May 1996, 271 (21): 12585–94. PMID 8647869. doi:10.1074/jbc.271.21.12585. 
6. McBride AE, Weiss VH, Kim HK, Hogle JM, Silver PA. Analysis of the yeast arginine methyltransferase Hmt1p/Rmt1p and its in vivo function. Cofactor binding and substrate interactions. J. Biol. Chem. February 2000, 275 (5): 3128–36. PMID 10652296. doi:10.1074/jbc.275.5.3128. 
7. 引证错误：没有为名为Branscombe的参考文献提供内容
8. 引证错误：没有为名为Weiss的参考文献提供内容
9. 引证错误：没有为名为Zhang的参考文献提供内容
10. McBride AE, Silver PA. State of the arg: protein methylation at arginine comes of age. Cell. July 2001, 106 (1): 5–8. PMID 11461695. doi:10.1016/S0092-8674(01)00423-8. 
11. Fersht AR, Sperling J. The charge relay system in chymotrypsin and chymotrypsinogen. J. Mol. Biol. February 1973, 74 (2): 137–49. PMID 4689953. doi:10.1016/0022-2836(73)90103-4. 
12. Chen F, Kan H, Castranova V. Methylation of Lysine 9 of Histone H3: Role of Heterochromatin Modulation and Tumorigenesis. Tollefsbol TO (编). Handbook of Epigenetics: The New Molecular and Medical Genetics. Boston: Academic Press. 2010: 149–157. ISBN 0-12-375709-6. doi:10.1016/B978-0-12-375709-8.00010-1. 
13. Espino PS, Drobic B, Dunn KL, Davie JR. Histone modifications as a platform for cancer therapy. J. Cell. Biochem. April 2005, 94 (6): 1088–102. PMID 15723344. doi:10.1002/jcb.20387. 
14. Hamamoto R, Furukawa Y, Morita M, Iimura Y, Silva FP, Li M, Yagyu R, Nakamura Y. SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells. Nat. Cell Biol. August 2004, 6 (8): 731–40. PMID 15235609. doi:10.1038/ncb1151. 

深入阅读

• Trievel RC. Structure and function of histone methyltransferases. Crit. Rev. Eukaryot. Gene Expr. 2004, 14 (3): 147–69. PMID 15248813. doi:10.1615/CritRevEukaryotGeneExpr.v14.i3.10. 
• Conde F, Refolio E, Cordón-Preciado V, Cortés-Ledesma F, Aragón L, Aguilera A, San-Segundo PA. The Dot1 histone methyltransferase and the Rad9 checkpoint adaptor contribute to cohesin-dependent double-strand break repair by sister chromatid recombination in Saccharomyces cerevisiae. Genetics. June 2009, 182 (2): 437–46. PMC 2691753  . PMID 19332880. doi:10.1534/genetics.109.101899. 

外部链接

• GeneReviews/NCBI/NIH/UW entry on Kleefstra Syndrome
• 醫學主題詞表（MeSH）：Histone-Lysine+N-Methyltransferase
• 醫學主題詞表（MeSH）：Protein-Arginine+N-Methyltransferase