Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
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DOI：
10.1073/pnas.0702981104
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发表时间：
2007-05-22
影响因子：
11.1
通讯作者：
Guo, Hong
中科院分区：
文献类型：
--
作者：
Guo, Hao-Bo;Guo, Hong
核小体核心组蛋白n端末端赖氨酸残基的甲基化对染色质结构和基因表达的调控具有重要意义。这种组蛋白修饰是由蛋白质赖氨酸甲基转移酶（PKMTs）催化的。在几乎所有的情况下，pkmt都含有一个保守的SET结构域，并可能将s -腺苷- l-蛋氨酸（AdoMet）的1到3个甲基转移到目标赖氨酸残基的e-氨基上。本文对人类PKMT SET7/9及其突变体进行了量子力学/分子力学分子动力学和自由能模拟，以了解PKMT催化反应的两个悬而未决的问题：带正电的甲基赖氨酸（lysine）去质子化的机制和产物特异性的来源。模拟结果表明，tyr335 （PKMTs中的一个绝对保守残基）可能在AdoMet与s -腺苷- l-同型半胱氨酸解离后和AdoMet结合前的去质子化过程中起着通用碱基的作用。结果表明，构象变化可使Y335到达目标甲基赖氨酸（赖氨酸）以进行质子提取。这一机制解释了pkmt催化甲基转移的过程性。报道并分析了野生型和某些突变体（Y305F和Y335F）的甲基转移自由能谱，并讨论了对酶的功能起重要作用的活性位点相互作用。模拟的结果为催化过程提供了重要的见解，并有助于更好地理解关于pkmt产物特异性起源的实验观察。
Methylation of certain lysine residues in the N-terminal tails of core histone proteins in nucleosome is of fundamental importance in the regulation of chromatin structure and gene expression. Such histone modification is catalyzed by protein lysine methyltransferases (PKMTs). PKMTs contain a conserved SET domain in almost all of the cases and may transfer one to three methyl groups from S-adenosyl-L-methionine (AdoMet) to the e-amino group of the target lysine residue. Here, quantum mechanical/molecular mechanical molecular dynamics and free-energy simulations are performed on human PKMT SET7/9 and its mutants to understand two outstanding questions for the reaction catalyzed by PKMTs: the mechanism for deprotonation of positively charged methyl lysine (lysine) and origin of product specificity. The results of the simulations suggest that Tyr-335 (an absolute conserved residue in PKMTs) may play the role as the general base for the deprotonation after dissociation of AdoHcy (S-adenosyl-L-homocysteine) and before binding of AdoMet. It is shown that conformational changes could bring Y335 to the target methyl lysine (lysine) for proton abstraction. This mechanism provides an explanation why methyl transfers could be catalyzed by PKMTs processively. The free-energy profiles for methyl transfers are reported and analyzed for wild type and certain mutants (Y305F and Y335F) and the active-site interactions that are of importance for the enzyme's function are discussed. The results of the simulations provide important insights into the catalytic process and lead to a better understanding of experimental observations concerning the origin of product specificity for PKMTs.