Lima Susana, Hildenbrand Jayne, Korostelev Andrei, Hattman Stanley, Li Hong
Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee 32306, USA.
RNA. 2002 Jul;8(7):924-32. doi: 10.1017/s1355838202028893.
The crystal structure of the 19-mer RNA, 5'-GAAUGCCUGCGAGCAUCCC-3' has been determined from X-ray diffraction data to 1.6 A resolution by the multiwavelength anomalous diffraction method from crystals containing a brominated uridine. In the crystal, this RNA forms an 18-mer self-complementary double helix with the 19th nucleotide flipped out of the helix. This helix contains most of the target stem recognized by the bacteriophage Mu Com protein (control of mom), which activates translation of an unusual DNA modification enzyme, Mom. The 19-mer duplex, which contains one A.C mismatch and one A.C/G.U tandem wobble pair, was shown to bind to the Com protein by native gel electrophoresis shift assay. Comparison of the geometries and base stacking properties between Watson-Crick base pairs and the mismatches in the crystal structure suggest that both hydrogen bonding and base stacking are important for stabilizing these mismatched base pairs, and that the unusual geometry adopted by the A.C mismatch may reveal a unique structural motif required for the function of Com.
通过多波长反常衍射法，利用含有溴化尿苷的晶体的X射线衍射数据，已确定19聚体RNA（5'-GAAUGCCUGCGAGCAUCCC-3'）的晶体结构，分辨率达到1.6埃。在晶体中，该RNA形成一个18聚体的自我互补双螺旋结构，第19个核苷酸从螺旋中翻转出来。这个螺旋包含噬菌体Mu Com蛋白（mom的控制因子）识别的大部分靶茎，该蛋白可激活一种特殊的DNA修饰酶Mom的翻译。通过天然凝胶电泳迁移分析表明，含有一个A·C错配和一个A·C/G·U串联摆动对的19聚体双链体与Com蛋白结合。晶体结构中沃森-克里克碱基对与错配之间的几何形状和碱基堆积性质的比较表明，氢键和碱基堆积对于稳定这些错配碱基对都很重要，并且A·C错配所采用的异常几何形状可能揭示了Com功能所需的独特结构基序。
