Heping Zheng1, Ivan G Shabalin2, Katarzyna B Handing3, Janusz M Bujnicki4, Wladek Minor5. 1. Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA Midwest Center for Structural Genomics (MCSG) Consortium, USA New York Structural Genomics Research Consortium (NYSGRC), USA. 2. Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA Midwest Center for Structural Genomics (MCSG) Consortium, USA New York Structural Genomics Research Consortium (NYSGRC), USA Enzyme Function Initiative (EFI), USA. 3. Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA Midwest Center for Structural Genomics (MCSG) Consortium, USA New York Structural Genomics Research Consortium (NYSGRC), USA Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland. 4. Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland. 5. Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA Midwest Center for Structural Genomics (MCSG) Consortium, USA New York Structural Genomics Research Consortium (NYSGRC), USA Enzyme Function Initiative (EFI), USA wladek@iwonka.med.virginia.edu.
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, Mg(2+)-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 Mg(2+) ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 'reliable' RNA-bound Mg(2+) sites. The normalized frequencies by which specific RNA atoms coordinate Mg(2+) were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg(2+) 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 Mg(2+)-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg(2+)-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs.
The ubiquitous presence of magnesium ions in RNA has long been recognized as a key n class="Gene">factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In this work, Mg(2+)-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 Mg(2+) ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 'reliable' RNA-bound Mg(2+) sites. The normalized frequencies by which specific RNA atoms coordinate Mg(2+) were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg(2+) 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 Mg(2+)-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg(2+)-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs.
Authors: H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971
Authors: Paul C D Hawkins; Gregory L Warren; A Geoffrey Skillman; Anthony Nicholls Journal: J Comput Aided Mol Des Date: 2008-01-23 Impact factor: 3.686
Authors: Maria A Borovinskaya; Raj D Pai; Wen Zhang; Barbara S Schuwirth; James M Holton; Go Hirokawa; Hideko Kaji; Akira Kaji; Jamie H Doudna Cate Journal: Nat Struct Mol Biol Date: 2007-07-29 Impact factor: 15.369
Authors: Anna Philips; Kaja Milanowska; Grzegorz Lach; Michal Boniecki; Kristian Rother; Janusz M Bujnicki Journal: Bioinformatics Date: 2011-11-21 Impact factor: 6.937
Authors: Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson Journal: Acta Crystallogr D Biol Crystallogr Date: 2009-12-21
Authors: P N Blank; A A Barnett; T A Ronnebaum; K E Alderfer; B N Gillott; D W Christianson; J A Himmelberger Journal: Acta Crystallogr D Struct Biol Date: 2020-05-29 Impact factor: 7.652
Authors: Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka Journal: Chem Rev Date: 2018-01-03 Impact factor: 60.622
Authors: Katarzyna B Handing; Ewa Niedzialkowska; Ivan G Shabalin; Misty L Kuhn; Heping Zheng; Wladek Minor Journal: Nat Protoc Date: 2018-04-19 Impact factor: 13.491