Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA.
Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA.
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DOI：
10.1042/bj20111885
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发表时间：
2012-03
期刊：
影响因子：
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通讯作者：
Y. Qiu;Wen Zhang;Chen Zhao;Yan Wang;Weiwei Wang;Jiahai Zhang;Zhiyong Zhang;Guohong Li;
中科院分区：
文献类型：
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作者：
Y. Qiu;Wen Zhang;Chen Zhao;Yan Wang;Weiwei Wang;Jiahai Zhang;Zhiyong Zhang;Guohong Li;
H4 K20（组蛋白H4的Lys（20））的甲基化在多种细胞过程的调节中起重要作用。在裂殖酵母中，H4 K20甲基化的所有三种状态都由Set 9催化。Pdp 1是一个含有PWWP（proline-tryptophan-proline）结构域的蛋白质，它与Set 9结合以调节Set 9的染色质定位和对H4 K20的甲基转移酶活性。在本研究中，通过溶液NMR确定了Pdp 1 PWWP结构域的结构，该结构域是第一个被鉴定的在H4 K20位点与甲基赖氨酸结合的PWWP结构域。Pdp 1 PWWP结构域采用经典的PWWP折叠，具有五条反向平行的β-桶，随后是三个α-螺旋。然而，它与其他PWWP结构域在某些结构方面有显着不同，部分原因是其分子识别。此外，我们还发现了PWWP结构域的独特结合模式，即Pdp 1的PWWP结构域不仅与组蛋白H4的三甲基化赖氨酸（20）H4 K20 me 3结合，而且还分别通过芳香笼和带正电荷的区域与双链DNA结合。EMSA（电泳迁移率变动分析）说明了Pdp 1 PWWP结构域结合核小体核心颗粒的能力，进一步的诱变实验表明这种结合活性在酵母细胞中组蛋白H4 K20二甲基化和三甲基化中的关键作用。本研究可能揭示了PWWP结构域调控组蛋白甲基化的新机制。
Methylation of H4K20 (Lys(20) of histone H4) plays an important role in the regulation of diverse cellular processes. In fission yeast, all three states of H4K20 methylation are catalysed by Set9. Pdp1 is a PWWP (proline-tryptophan-tryptophan-proline) domain-containing protein, which associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. The structure of the Pdp1 PWWP domain, which is the first PWWP domain identified which binds to methyl-lysine at the H4K20 site, was determined in the present study by solution NMR. The Pdp1 PWWP domain adopts a classical PWWP fold, with a five-strand antiparallel β-barrel followed by three α-helices. However, it differs significantly from other PWWP domains in some structural aspects that account, in part, for its molecular recognition. Moreover, we revealed a unique binding pattern of the PWWP domain, in that the PWWP domain of Pdp1 bound not only to H4K20me3 (trimethylated Lys(20) of histone H4), but also to dsDNA (double-stranded DNA) via an aromatic cage and a positively charged area respectively. EMSAs (electrophoretic mobility-shift assays) illustrated the ability of the Pdp1 PWWP domain to bind to the nucleosome core particle, and further mutagenesis experiments indicated the crucial role of this binding activity in histone H4K20 di- and tri-methylation in yeast cells. The present study may shed light on a novel mechanism of histone methylation regulation by the PWWP domain.