Structural basis for human PHF2 Jumonji domain interaction with metal ions.
Structural basis for human PHF2 Jumonji domain interaction with metal ions.
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人类PHF2 Jumonji结构域与金属离子相互作用的结构基础。
DOI：
10.1016/j.jmb.2010.12.013
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发表时间：
2011-02-11
影响因子：
5.6
通讯作者：
Cheng X
中科院分区：
文献类型：
--
作者：
Horton JR;Upadhyay AK;Hashimoto H;Zhang X;Cheng X
PHF 2属于一类α-酮戊二酸-Fe 2+依赖性双加氧酶。PHF 2具有植物同源结构域（PHD）和Jumonji结构域。PHF 2通过其PHD结构域以亚微摩尔亲和力结合Lys 4-三甲基化组蛋白3（H3 K4 me 3），并且已报道在体内具有组蛋白3的单甲基化赖氨酸9（H3 K9 me 1）的脱甲基酶活性。然而，在组蛋白肽的背景下，我们没有检测到PHF 2 Jumonji结构域（有和没有其连接的PHD）的脱甲基酶活性。我们确定的晶体结构的PHF 2 Jumonji域的存在和不存在额外的外源金属离子。只有当暴露于高金属浓度（50 mM），Fe 2+或Ni 2+浸泡到预成型的晶体和结合的六个配体在八面体协调。H249、D251的侧链和N-草酰甘氨酸（α-酮戊二酸的类似物）的两个氧原子在赤道平面上提供四个配位，而Y321的羟基氧原子和一个水分子分别作为第五和第六配体提供两个轴向配位。PHF 2中的金属结合位点与其他Jumonji结构域中的Fe 2+位点非常相似，但有一个重要的区别，即酪氨酸（PHF 2的Y321）取代组氨酸作为第五配体。然而，无论是Y321 H突变，也没有高浓度的金属使PHF 2的组蛋白肽的活性脱甲基酶。野生型和Y321 H突变体都以大约相等的50 µM亲和力结合Ni 2+。我们认为PHF 2在体内的酶活性还需要其他的调节因子，或者PHF 2作用于非组蛋白底物。此外，PHF 2在整个区域中与裂殖酵母Epe 1共享显著的序列同源物，包括在相应的铁结合位置处的上述酪氨酸，裂殖酵母Epe 1在异染色质功能中起重要作用，但也没有已知的酶活性。
PHF2 belongs to a class of α-ketoglutarate-Fe2+–dependent dioxygenases. PHF2 harbors a plant homeodomain (PHD) and a Jumonji domain. PHF2, via its PHD domain, binds Lys4-trimethylated histone 3 (H3K4me3) in sub micromolar affinity, and has been reported to have demethylase activity of mono-methylated lysine 9 of histone 3 (H3K9me1) in vivo. However, we did not detect demethylase activity for PHF2 Jumonji domain (with and without its linked PHD) in the context of histone peptides. We determined the crystal structures of PHF2 Jumonji domain in the absence and presence of additional exogenous metal ions. Only when exposed to high metal concentration (50 mM), Fe2+ or Ni2+ was soaked into the preformed crystals and bound by six ligands in an octahedral coordination. The side-chains of H249, D251, and the two oxygen atoms of N-oxalylglycine (an analog of α-ketoglutarate) provide four coordinations in the equatorial plane, while the hydroxyl oxygen atom of Y321 and one water molecule provide the two axial coordinations as the fifth and sixth ligands, respectively. The metal binding site in PHF2 closely resembles the Fe2+ sites in other Jumonji domains examined, with one important difference, that a tyrosine (Y321 of PHF2) replaces a histidine as the fifth ligand. However, neither Y321H mutation nor high metal concentration renders PHF2 an active demethylase on histone peptides. Both wild type and Y321H mutant bind Ni2+ with approximately equal affinity of 50 µM. We propose there must be other regulatory factors required for the enzymatic activity of PHF2 in vivo, or perhaps PHF2 acts on non-histone substrates. Furthermore, PHF2 shares significant sequence homolog throughout the entire region, including the above-mentioned tyrosine at the corresponding iron-binding position, with that of Schizosaccharomyces pombe Epe1, which plays essential role in heterochromatin function but also has no known enzymatic activity.
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