Structure of a double-stranded DNA (6–4) photoproduct in complex with the 64M-5 antibody Fab.
Structure of a double-stranded DNA (6–4) photoproduct in complex with the 64M-5 antibody Fab.
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与 64M-5 抗体 Fab 复合的双链 DNA (6–4) 光产物的结构。
DOI：
10.1107/s0907444912050007
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发表时间：
2013
期刊：
影响因子：
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通讯作者：
Yoshinori Satow
中科院分区：
文献类型：
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作者：
Hideshi Yokoyama;Ryuta Mizutani;Yoshinori Satow
紫外线辐射形成的（6-4）嘧啶-嘧啶酮加合物的DNA光产物与诱变和癌症有关。在2.5 μ m分辨率下测定了含有与抗-（6 - 4）-光产物抗体64 M-5 Fab复合的（6 - 4）-光产物的双链DNA的晶体结构。 T（6-4）T片段和5′端相邻的腺苷从双链体中翻转出来，并容纳在由6个互补决定区（CDR）组成的凹形抗原结合口袋中。在翻转的T（6-4）T区段和互补DNA之间插入由CDR L1残基组成的环。通过插入环而使链分离，有利于光产物的广泛和特异性识别。T（6-4）T片段两侧的DNA螺旋以87°扭结。64 M-5 Fab识别从互补链解离的T（6-4）T片段，表明使用64 M-5抗体可以在双链DNA和单链DNA中检测（6-4）光产物。将6 - 4 M-5抗体的结构和识别模式与DNA（6-4）光裂合酶和核苷酸切除修复蛋白DDB 1-DDB 2的结构和识别模式进行了比较。这些蛋白质具有与其功能相适应的独特结合位点结构，并且光损伤的翻转和DNA的扭结对于蛋白质识别的诱变（6-4）光产物是常见的。
DNA photoproducts with (6–4) pyrimidine–pyrimidone adducts formed by ultraviolet radiation have been implicated in mutagenesis and cancer. The crystal structure of double-stranded DNA containing the (6–4) photoproduct in complex with the anti-(6–4)-photoproduct antibody 64M-5 Fab was determined at 2.5 Å resolution. The T(6–4)T segment and the 5′-side adjacent adenosine are flipped out of the duplex and are accommodated in the concave antigen-binding pocket composed of six complementarity-determining regions (CDRs). A loop comprised of CDR L1 residues is inserted between the flipped-out T(6–4)T segment and the complementary DNA. The separation of strands by the insertion of the loop facilitates extensive and specific recognition of the photoproduct. The DNA helices flanking the T(6–4)T segment are kinked by 87°. The 64M-5 Fab recognizes the T(6–4)T segment dissociated from the complementary strand, indicating that the (6–4) photoproduct can be detected in double-stranded DNA as well as in single-stranded DNA using the 64M-5 antibody. The structure and recognition mode of the 64M-5 antibody were compared with those of the DNA (6–4) photolyase and nucleotide-excision repair protein DDB1–DDB2. These proteins have distinctive binding-site structures that are appropriate for their functions, and the flipping out of the photolesion and the kinking of the DNA are common to mutagenic (6–4) photoproducts recognized by proteins.