Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6A resolution
Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6A resolution
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DOI：
10.1093/nar/gkm139
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发表时间：
2007-04-01
影响因子：
14.9
通讯作者：
James, Thomas L.
中科院分区：
文献类型：
--
作者：
Fenn, Sebastian;Du, Zhihua;James, Thomas L.
KH（hnRNP K homology）结构域存在于多种核酸结合蛋白中，由约70个氨基酸残基组成。其中包括多聚（C）结合蛋白（PCBP），它们是mRNA稳定性和转录后调控的重要调节因子。所有PCBP都含有三个不同的KH结构域，并以高亲和力和特异性识别poly（C）序列。为了揭示poly（C）-序列识别的分子基础，我们在1.6埃分辨率下测定了PCBP 2 KH 3结构域与7-nt DNA序列（5 '-AACCTA-3 '）复合物的晶体结构，该序列对应于人端粒DNA的一个富C链重复序列。该结构域假定为β α α β β α构型的I型KH折叠。蛋白质-DNA界面可以被前所未有的详细研究，并且由蛋白质和DNA之间的一系列直接和水介导的氢键组成，揭示了一个特别密集的网络，涉及核心识别序列中最后2个核苷酸的几个结构水分子。与已发表的KH结构域结构不同，该蛋白质在没有蛋白质-蛋白质接触的情况下结晶，从而对不同KH结构域的二聚化性质产生了新的见解。在一些RNA分子中发现的一个有趣的特征是核苷酸平台，这显然是DNA中的第一次。
KH (hnRNP K homology) domains, consisting of similar to 70 amino acid residues, are present in a variety of nucleic-acid-binding proteins. Among these are poly(C)-binding proteins (PCBPs), which are important regulators of mRNA stability and posttranscriptional regulation in general. All PCBPs contain three different KH domains and recognize poly(C)sequences with high affinity and specificity. To reveal the molecular basis of poly(C)-sequence recognition, we have determined the crystal structure, at 1.6 angstrom resolution, of PCBP2 KH3 domain in complex with a 7-nt DNA sequence (5 '-AACCCTA-3 ') corresponding to one repeat of the C-rich strand of human telomeric DNA. The domain assumes a type-I KH fold in a beta alpha alpha beta beta alpha configuration. The protein-DNA interface could be studied in unprecedented detail and is made up of a series of direct and water-mediated hydrogen bonds between the protein and the DNA, revealing an especially dense network involving several structural water molecules for the last 2 nt in the core recognition sequence. Unlike published KH domain structures, the protein crystallizes without protein-protein contacts, yielding new insights into the dimerization properties of different KH domains. A nucleotide platform, an interesting feature found in some RNA molecules, was identified, evidently for the first time in DNA.