Abstract
The ubiquitous presence of magnesium ions in RNA has long been recognized as a key factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In this work, Mg2+-binding architectures in RNA were systematically studied using a database of RNA crystal structures from the Protein Data Bank (PDB). Due to the abundance of poorly modeled or incorrectly identified Mg2+ ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 ‘reliable’ RNA-bound Mg2+ sites. The normalized frequencies by which specific RNA atoms coordinate Mg2+ were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg2+ sites in RNA structures was designed and applied to the benchmark dataset, yielding a set of 41 types of inner-sphere and 95 types of outer-sphere coordinating patterns. This classification system has also been applied to describe six previously reported Mg2+-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg2+-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs.
Highlights
Metal ions are indispensable for proper RNA folding, stability and function in various biological processes [1]
The majority of the non-ribosome structures contain fewer than 10 Mg2+ sites each (Figure 2). This trend indicates that the number of modeled Mg2+ sites located by X-ray crystallography is often insufficient to neutralize the negative charge of RNA due to diffusely bound Mg2+, presence of other cations, limited resolution of the crystal structure and/or difficulty in Mg2+ identification
We sought to identify and analyze ‘validated motifs,’ which we considered to be a specific structural arrangement provided by RNA for Mg2+ binding, which is found in structures of multiple RNA molecules
Summary
Metal ions are indispensable for proper RNA folding, stability and function in various biological processes [1]. The resulting structural complexity and wide repertoire of structural arrangements allows RNA to effectively perform a multitude of key cellular functions. In addition to their ubiquitous role as counter ions, metal ions are crucial for some RNA molecules to recognize binding partners [3,4]. Recent advancements in macromolecule crystallography have led to the determination of many structurally diverse metal-containing RNA crystal structures, offering a unique opportunity for such a survey of Mg2+ binding sites
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