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Solution structure and metal ion binding sites of the human CPEB3 ribozyme’s P4 domain

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Publication date 2014
Author Skilandat Miriam, Rowinska-Zyrek Magdalena, Sigel Roland K. O.,
Project Metal Ion-Guided Assembly and Structures of the Catalytic Core of Ribozymes
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Original article (peer-reviewed)

Journal JBIC Journal of Biological Inorganic Chemistry
Volume (Issue) 19(6)
Page(s) 903 - 912
Title of proceedings JBIC Journal of Biological Inorganic Chemistry
DOI 10.1007/s00775-014-1125-6


Three ribozymes are known to occur in humans, the CPEB3 ribozyme, the CoTC ribozyme, and the hammerhead ribozyme. Here, we present the NMR solution structure of a well-conserved motif within the CPEB3 ribozyme, the P4 domain. In addition, we discuss the binding sites and impact of Mg2+ and [Co(NH3)6]3+, a spectroscopic probe for [Mg(H2O)6]2+, on the structure. The well-defined P4 region is a hairpin closed with a UGGU tetraloop that shows a distinct electrostatic surface potential and a characteristic, strongly curved backbone trajectory. The P4 hairpin contains two specific Mg2+ binding sites: one outer-sphere binding site close to the proposed CPEB3 ribozyme active site with potential relevance for maintaining a compact fold of the ribozyme core, and one inner-sphere binding site, probably stabilizing the tetraloop structure. The structure of the tetraloop resembles an RNase III recognition structure, as previously described for an AGUU tetraloop. The detailed knowledge of the P4 domain and its metal ion binding preferences thus brings us closer to understanding the importance of Mg2+ binding for the CPEB3 ribozyme’s fold and function in the cell.