MINAS—a database of Metal Ions in Nucleic AcidS

Schnabl, Joachim; Suter, Pascal; Sigel, Roland K. O.

doi:10.1093/nar/gkr920

Cited by 36 publications

(32 citation statements)

References 15 publications

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“…This indicates that a Mg 2ϩ ion might be able to move slightly within this binding region by exchanging some of its hydration shell with nucleic acid ligands. Such partial inner sphere coordination is well in line with crystal structures of RNAs in general, which show that the vast majority of Mg 2ϩ ions are partially dehydrated (102,103). In general, the combination of the kink in the sugar phosphate backbone at G13 and the short and tunnel-shaped major groove of EBS1⅐dIBS1 seems ideal to attract metal ions because it provides a suitable shape and accumulates negative charge in a small region.…”

Section: Discussionsupporting

confidence: 75%

The Role of Mg(II) in DNA Cleavage Site Recognition in Group II Intron Ribozymes

Skilandat

Sigel

2014

Journal of Biological Chemistry

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Background: Group II introns cleave DNA and RNA 3Ј of a short duplex formed between the intron and the target. Results: We present the NMR structure of this hybrid duplex and describe two distinct Mg 2ϩ binding sites. Conclusion:The hybrid is asymmetric and strongly stabilized by Mg 2ϩ binding. Significance: Site-bound metal ions are crucially important for group II intron cleavage site recognition.

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Section: Discussionsupporting

confidence: 75%

The Role of Mg(II) in DNA Cleavage Site Recognition in Group II Intron Ribozymes

Skilandat

Sigel

2014

Journal of Biological Chemistry

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“…The structural overlay (Fig. 5C) reveals that M C has moved away from G in the (E•S•G) O model and does not form the inner-sphere contacts (≤2.5 Å) (Schnabl et al 2012) made with the -OH groups in the (E•S•G) C complex. The models also suggest a modest (∼0.95 Å) change in the position of M A .…”

Section: Is the Reactive Phosphoryl Group On S Responsible For The DImentioning

confidence: 99%

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

Sengupta

Schie

Giambaşu

et al. 2015

RNA

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Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2 ′ -and 3 ′ -deoxy (-H) and −amino (-NH 2 ) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3 ′ -OH making a nonproductive interaction with an active site metal ion termed M A and with the adjacent 2 ′ -OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M C , to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function.

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“…MINAS (http://www.minas.uzh.ch/) (6) focuses on metal–nucleic acid interactions, and thus it does not include metalloproteins. Thus MetalPDB and MINAS can be seen as complementary, with some limited overlap.…”

Section: Comparison With Other Available Databases Focusing On Metalsmentioning

confidence: 99%

MetalPDB: a database of metal sites in biological macromolecular structures

Andreini

Cavallaro

Lorenzini

et al. 2012

Nucleic Acids Research

173

154

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We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal–macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.

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MINAS—a database of Metal Ions in Nucleic AcidS

Cited by 36 publications

References 15 publications

The Role of Mg(II) in DNA Cleavage Site Recognition in Group II Intron Ribozymes

The Role of Mg(II) in DNA Cleavage Site Recognition in Group II Intron Ribozymes

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

MetalPDB: a database of metal sites in biological macromolecular structures

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