Devany Matthew, Kappes Ferdinand, Chen Kuan-Ming, Markovitz David M, Matsuo Hiroshi
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
Protein Sci. 2008 Feb;17(2):205-15. doi: 10.1110/ps.073244108.
The human DEK protein has a long-standing association with carcinogenesis since the DEK gene was originally identified in the t(6:9) chromosomal translocation in a subtype of patients with acute myelogenous leukemia (AML). Recent studies have partly unveiled DEK's cellular functions including apoptosis inhibition in primary cells as well as cancer cells, determination of 3' splice site of transcribed RNA, and suppression of transcription initiation by polymerase II. It has been previously shown that the N-terminal region of DEK, spanning residues 68-226, confers important in vitro and in vivo functions of DEK, which include double-stranded DNA (ds-DNA) binding, introduction of constrained positive supercoils into closed dsDNA, and apoptosis inhibition. In this paper, we describe the three-dimensional structure of the N-terminal domain of DEK (DEKntd) as determined using solution NMR. The C-terminal part of DEKntd, which contains a putative DNA-binding motif (SAF/SAP motif), folds into a helix-loop-helix structure. Interestingly, the N-terminal part of DEKntd shows a very similar structure to the C-terminal part, although the N-terminal and the C-terminal part differ distinctively in their amino acid sequences. As a consequence, the structure of DEKntd has a pseudo twofold plane symmetry. In addition, we tested dsDNA binding of DEKntd by monitoring changes of NMR chemical shifts upon addition of dsDNAs. We found that not only the C-terminal part containing the SAF/SAP motif but the N-terminal part is also involved in DEKntd's dsDNA binding. Our study illustrates a new structural variant and reveals novel dsDNA-binding properties for proteins containing the SAP/SAF motif.
自DEK基因最初在急性髓性白血病（AML）患者的一个亚型的t(6;9)染色体易位中被鉴定以来，人类DEK蛋白就一直与致癌作用相关。最近的研究部分揭示了DEK的细胞功能，包括对原代细胞和癌细胞凋亡的抑制、转录RNA 3'剪接位点的确定以及聚合酶II对转录起始的抑制。先前已经表明，DEK的N端区域（跨越第68至226位残基）赋予了DEK重要的体外和体内功能，其中包括双链DNA（ds-DNA）结合、将受限的正超螺旋引入闭合的dsDNA以及凋亡抑制。在本文中，我们描述了使用溶液核磁共振确定的DEK N端结构域（DEKntd）的三维结构。DEKntd的C端部分包含一个假定的DNA结合基序（SAF/SAP基序），折叠成螺旋-环-螺旋结构。有趣的是，DEKntd的N端部分显示出与C端部分非常相似的结构，尽管N端和C端部分在氨基酸序列上有明显差异。因此，DEKntd的结构具有伪二重平面对称性。此外，我们通过监测添加dsDNA后NMR化学位移的变化来测试DEKntd与dsDNA的结合。我们发现，不仅包含SAF/SAP基序的C端部分，而且N端部分也参与了DEKntd与dsDNA的结合。我们的研究阐明了一种新的结构变体，并揭示了含有SAP/SAF基序的蛋白质的新型dsDNA结合特性。
