Nishinaka T, Shinohara A, Ito Y, Yokoyama S, Shibata T
Cellular and Molecular Biology Laboratory, The Institute of Physical and Chemical Research (RIKEN), Saitama 351-0198, Japan.
Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11071-6. doi: 10.1073/pnas.95.19.11071.
Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions are essential for homologous genetic recombination in various organisms. From NMR studies, we previously reported a novel deoxyribose-base stacking interaction between adjacent residues on the extended single-stranded DNA bound to RecA protein. In this study, we found that the same DNA structure was induced by the binding to Saccharomyces cerevisiae Rad51 protein, indicating that the unique DNA structure induced by the binding to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of this structure, we have formulated the structure of duplex DNA within filaments formed by RecA protein and its homologs. Two types of molecular structures are presented. One is the duplex structure that has the N-type sugar pucker. Its helical pitch is approximately 95 A (18.6 bp/turn), corresponding to that of an active, or ATP-form of the RecA filament. The other is one that has the S-type sugar pucker. Its helical pitch is approximately 64 A (12.5 bp/turn), corresponding to that of an inactive, or ADP-form of the RecA filament. During this modeling, we found that the interconversion of sugar puckers between the N-type and the S-type rotates bases horizontally, while maintaining the deoxyribose-base stacking interaction. We propose that this base rotation enables base pair switching between double-stranded DNA and single-stranded DNA to take place, facilitating homologous pairing and strand exchange. A possible mechanism for strand exchange involving DNA rotation also is discussed.
大肠杆菌RecA是RecA家族蛋白质的代表，该家族蛋白质促进双链DNA与单链DNA之间的同源配对和链交换。这些反应对于各种生物体中的同源基因重组至关重要。通过核磁共振研究，我们之前报道了与RecA蛋白结合的延伸单链DNA上相邻残基之间存在一种新型的脱氧核糖-碱基堆积相互作用。在本研究中，我们发现与酿酒酵母Rad51蛋白结合也能诱导出相同的DNA结构，这表明与RecA同源物结合所诱导的独特DNA结构从原核生物到真核生物都是保守的。基于这种结构，我们构建了由RecA蛋白及其同源物形成的细丝内双链DNA的结构。提出了两种分子结构。一种是具有N型糖构象的双链结构。其螺旋螺距约为95埃（每圈18.6个碱基对），与RecA细丝的活性形式或ATP形式相对应。另一种是具有S型糖构象的结构。其螺旋螺距约为64埃（每圈12.5个碱基对），与RecA细丝的非活性形式或ADP形式相对应。在这个建模过程中，我们发现N型和S型糖构象之间的相互转换会使碱基水平旋转，同时保持脱氧核糖-碱基堆积相互作用。我们提出这种碱基旋转使得双链DNA与单链DNA之间能够发生碱基对切换，从而促进同源配对和链交换。还讨论了涉及DNA旋转的链交换的可能机制。
