Crystal structure of a free κB DNA:: Insights into DNA recognition by transcription factor NF-κB
Crystal structure of a free κB DNA:: Insights into DNA recognition by transcription factor NF-κB
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DOI：
10.1016/j.jmb.2004.11.042
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发表时间：
2005-02-11
影响因子：
5.6
通讯作者：
Ghosh, G
中科院分区：
文献类型：
--
作者：
Huang, DB;Phelps, CB;Ghosh, G
二聚体NF-kappaB转录因子通过识别靶基因启动子内的特定DNA序列来调节基因表达。被称为kappaB DNA的DNA序列被分为两大类。I类kappaB DNA最适合与NF-kappaB亚基p50和p52结合，而II类kappaB DNA则被NF-kappaB亚基c-Rel和p65特异性识别。我们以1.60埃的分辨率测定了II类kappaB DNA序列的x射线晶体结构。这个结构提供了kappaB DNA水合作用、反离子结合和在没有NF-kappaB结合伙伴的情况下的构象的详细图片。先前已经确定了与NF-kappaB二聚体结合的I类和II类kappaB DNA的x射线结构。此外，一类kappaB DNA的核磁共振溶液结构是已知的。结合蛋白和未结合的kappaB DNA结构的比较表明，这两类的自由形式更接近理想的b型DNA。特定DNA碱基的局部几何形状在与nf - κ b结合时显著不同。这在5'-GG/CC碱基对上尤为明显；NF-kappaB特异性DNA结合序列的特征。在结合和未结合的kappaB DNA之间观察到不同的磷酸基团构象、小凹槽宽度、扣、扭和倾斜角度。我们观察到，在I类kappaB DNA的GGA序列上存在一个额外的G:C碱基对5'-，改变了GGGA四核苷酸中两个内部G:C碱基对的几何形状，这至少部分解释了两种不同类型的kappaB DNA募集不同NF-kappaB二聚体的结构基础。总之，这些观察结果表明，NF-kappaB二聚体识别kappaB DNA的特定结构特征，以形成序列特异性复合物。(C) 2004 Elsevier Ltd.版权所有。
The dimeric NF-kappaB transcription factors regulate gene expression by recognizing specific DNA sequences located within the promoters of target genes. The DNA sequences, referred to as kappaB DNA, are divided into two broad classes. Class I kappaB DNA binds optimally to p50 and p52 NF-kappaB subunits, while class II kappaB DNAs are recognized specifically by the NF-kappaB subunits c-Rel and p65. We determined the X-ray crystal structure of a class II kappaB DNA sequence at 1.60 Angstrom resolution. This structure provides a detailed picture Of kappaB DNA hydration, counter ion binding, and conformation in the absence of NF-kappaB binding partner. X-ray structures of both class I and class II kappaB DNA bound to NF-kappaB dimers were determined previously. Additionally, the NMR solution structure of a class I kappaB DNA is known. Comparison of the protein-bound and unbound kappaB DNA structures reveals that the free form of both classes approximates ideal B-form DNA more closely. Local geometries about specific DNA bases differ significantly upon binding to NF-kappaB. This is particularly evident at the 5'-GG/CC base-pairs; a signature of NF-kappaB specific DNA binding sequences. Differential phosphate group conformations, minor groove widths, buckle, twist, and tilt angles are observed between bound and unbound kappaB DNA. We observe that the presence of an extra G:C base-pair, 5'- to the GGA sequence in class I kappaB DNA, alters the geometry of the two internal G:C base-pairs within the GGGA tetranucleotide, which explains, at least in part, the structural basis for distinct NF-kappaB dimer recruitment by the two different classes of kappaB DNA. Together, these observations suggest that NF-kappaB dimers recognize specific structural features of kappaB DNA in order to make sequence-specific complexes. (C) 2004 Elsevier Ltd. All rights reserved.