Crystal structure of a zinc-finger-RNA complex reveals two modes of molecular recognition.
Zinc-finger proteins of the classical Cys2His2 type are the most frequently used class of transcription factor and account for about 3% of genes in the human genome. The zinc-finger motif was discovered during biochemical studies on the transcription factor TFIIIA, which regulates the 5S ribosomal RNA genes of Xenopus laevis. Zinc-fingers mostly interact with DNA, but TFIIIA binds not only specifically to the promoter DNA, but also to 5S RNA itself. Increasing evidence indicates that zinc-fingers are more widely used to recognize RNA. There have been numerous structural studies on DNA binding, but none on RNA binding by zinc-finger proteins. Here we report the crystal structure of a three-finger complex with 61 bases of RNA, derived from the central regions of the complete nine-finger TFIIIA-5S RNA complex. The structure reveals two modes of zinc-finger binding, both of which differ from that in common use for DNA: first, the zinc-fingers interact with the backbone of a double helix; and second, the zinc-fingers specifically recognize individual bases positioned for access in otherwise intricately folded 'loop' regions of the RNA.
Lu
Duo
D
Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, UK.
Searles
M Alexandra
MA
Klug
Aaron
A
D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012341:RNA, Ribosomal, 5S / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity; D035582:Transcription Factor TFIIIA / Q000737:chemistry* / Q000378:metabolism*; D016335:Zinc Fingers / Q000502:physiology*
D012341:RNA, Ribosomal, 5S; D035582:Transcription Factor TFIIIA