ArticleBiochemistry2011
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Evidence for Hidden Involvement of N3-Protonated Guanine in RNA Structure and Function.ACS omega · 2019Article
- Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.Nucleic acids research · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.Biochemistry · 2016Article
- 'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.Nucleic acids research · 2016Article
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 2015Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density.Biochemistry · 2015Article
- Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.Physical chemistry chemical physics : PCCP · 2015Article
- Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations.Journal of the American Chemical Society · 2015Article
- The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.Physical chemistry chemical physics : PCCP · 2015Article
- New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.Nucleic acids research · 2014Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.Journal of the American Chemical Society · 2014Article
- Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.The journal of physical chemistry. B · 2013Article
- Thermodynamic and structural determinants of differential Pdx1 binding to elements from the insulin and IAPP promoters.Journal of molecular biology · 2013Article
- Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme.Biochemistry · 2013Article
- Article
- Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.The journal of physical chemistry. B · 2012Article
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6 authors.
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Abstract
The hepatitis delta virus (HDV) ribozyme uses both metal ion and nucleobase catalysis in its cleavage mechanism. A reverse G·U wobble was observed in a recent crystal structure of the precleaved state. This unusual base pair positions a Mg(2+) ion to participate in catalysis. Herein, we used molecular dynamics (MD) and X-ray crystallography to characterize the conformation and metal binding characteristics of this base pair in product and precleaved forms. Beginning with a crystal structure of the product form, we observed formation of the reverse G·U wobble during MD trajectories. We also demonstrated that this base pair is compatible with the diffraction data for the product-bound state. During MD trajectories of the product form, Na(+) ions interacted with the reverse G·U wobble in the RNA active site, and a Mg(2+) ion, introduced in certain trajectories, remained bound at this site. Beginning with a crystal structure of the precleaved form, the reverse G·U wobble with bound Mg(2+) remained intact during MD simulations. When we removed Mg(2+) from the starting precleaved structure, Na(+) ions interacted with the reverse G·U wobble. In support of the computational results, we observed competition between Na(+) and Mg(2+) in the precleaved ribozyme crystallographically. Nonlinear Poisson-Boltzmann calculations revealed a negatively charged patch near the reverse G·U wobble. This anionic pocket likely serves to bind metal ions and to help shift the pK(a) of the catalytic nucleobase, C75. Thus, the reverse G·U wobble motif serves to organize two catalytic elements, a metal ion and catalytic nucleobase, within the active site of the HDV ribozyme.
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