(Q43541902)

PubMed publication ID

24 November 2017

1 reference

title

Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

13 May 2020

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

13 May 2020

language of work or name

English

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publication date

6 August 2010

1 reference

PubMed publication ID

24 November 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

13 May 2020

volume

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

13 May 2020

issue

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

13 May 2020

page(s)

5389-5407

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

Creative Commons Attribution 4.0 International

13 May 2020

copyright license

start time

6 August 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

1 reference

12 December 2020

Characterization of a native hammerhead ribozyme derived from schistosomes

1 reference

12 December 2020

Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site

1 reference

12 December 2020

Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration

1 reference

12 December 2020

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction

1 reference

12 December 2020

The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage

1 reference

12 December 2020

Application of a 5'-bridging phosphorothioate to probe divalent metal and hammerhead ribozyme mediated RNA cleavage

1 reference

12 December 2020

Controlling ribozyme activity by metal ions

1 reference

12 December 2020

Ribozyme catalysis revisited: is water involved?

1 reference

12 December 2020

1 reference

12 December 2020

Double-Metal-Ion/Single-Metal-Ion Mechanisms of the Cleavage Reaction of Ribozymes: First-Principles Molecular Dynamics Simulations of a Fully Hydrated Model System.

1 reference

12 December 2020

Can a hydroxide ligand trigger a change in the coordination number of magnesium ions in biological systems?

1 reference

12 December 2020

Analysis of solvent nucleophile isotope effects: evidence for concerted mechanisms and nucleophilic activation by metal coordination in nonenzymatic and ribozyme-catalyzed phosphodiester hydrolysis

1 reference

12 December 2020

Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis

1 reference

12 December 2020

An equivalent metal ion in one- and two-metal-ion catalysis

1 reference

12 December 2020

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme

1 reference

12 December 2020

Sites and thermodynamic quantities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and and nucleotides

1 reference

12 December 2020

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

1 reference

12 December 2020

Comparative enzymology and structural biology of RNA self-cleavage

1 reference

12 December 2020

The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme

1 reference

12 December 2020

Cloning and characterization of extended hammerheads from a diverse set of caudate amphibians.

1 reference

12 December 2020

Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site

1 reference

12 December 2020

Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism

1 reference

12 December 2020

NMR structure of varkud satellite ribozyme stem-loop V in the presence of magnesium ions and localization of metal-binding sites

1 reference

12 December 2020

Crystal structure of a hepatitis delta virus ribozyme

1 reference

12 December 2020

Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme

1 reference

12 December 2020

Solvent Structure and Hammerhead Ribozyme Catalysis

1 reference

12 December 2020

Solvent Protection of the Hammerhead Ribozyme in the Ground State: Evidence for a Cation-Assisted Conformational Change Leading to Catalysis

1 reference

12 December 2020

The distribution of RNA motifs in natural sequences

1 reference

12 December 2020

Transition state stabilization by a catalytic RNA

1 reference

12 December 2020

Ligand-pKa shifts through metals: potential relevance to ribozyme chemistry

1 reference

12 December 2020

The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a

1 reference

12 December 2020

Probing general base catalysis in the hammerhead ribozyme

1 reference

12 December 2020

Structure-function relationships in RNA and RNP enzymes: recent advances

1 reference

12 December 2020

Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites

1 reference

12 December 2020

NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.

1 reference

12 December 2020

Structural evidence for a two-metal-ion mechanism of group I intron splicing

1 reference

12 December 2020

In vitro evolution suggests multiple origins for the hammerhead ribozyme

1 reference

12 December 2020

A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme

1 reference

12 December 2020

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

1 reference

12 December 2020

Ribozyme-mediated cleavage of a substrate analogue containing an internucleotide-bridging 5'-phosphorothioate: evidence for the single-metal model

1 reference

12 December 2020

Metal ions in the structure and function of RNA.

1 reference

12 December 2020

RNA folding and catalysis

1 reference

12 December 2020

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

1 reference

12 December 2020

Recent advances in the elucidation of the mechanisms of action of ribozymes

1 reference

12 December 2020

Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme

1 reference

12 December 2020

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme

1 reference

12 December 2020

Investigating metal-binding in proteins by nuclear magnetic resonance.

1 reference

12 December 2020

Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis

1 reference

12 December 2020

Catalytic importance of a protonated adenosine in the hairpin ribozyme active site

1 reference

12 December 2020

Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme

1 reference

12 December 2020

Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

1 reference

12 December 2020

Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank.

1 reference

12 December 2020

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

1 reference

12 December 2020

Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis

1 reference

12 December 2020

Relating conformation, Mg2+ binding, and functional group modification in the hammerhead ribozyme

1 reference

12 December 2020

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

1 reference

12 December 2020

Hammerhead redux: does the new structure fit the old biochemical data?

1 reference

12 December 2020

Structure and dynamics of the hydrated magnesium ion and of the solvated magnesium carbonates: insights from first principles simulations.

1 reference

12 December 2020

Computer simulations of enzyme catalysis: methods, progress, and insights

1 reference

12 December 2020

Coordination environment of a site-bound metal ion in the hammerhead ribozyme determined by 15N and 2H ESEEM spectroscopy.

1 reference

12 December 2020

Crystal Structure of a Self-Spliced Group II Intron

1 reference

12 December 2020

Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

1 reference

12 December 2020

Extraordinary rates of transition metal ion-mediated ribozyme catalysis

1 reference

12 December 2020

A general two-metal-ion mechanism for catalytic RNA

1 reference

12 December 2020

Structural metals in the group I intron: a ribozyme with a multiple metal ion core

1 reference

12 December 2020

Probing general acid catalysis in the hammerhead ribozyme.

1 reference

12 December 2020

Detection of RNA nucleobase metalation by NMR spectroscopy

1 reference

12 December 2020

Trapped water molecules are essential to structural dynamics and function of a ribozyme

1 reference

12 December 2020

Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change

1 reference

12 December 2020

Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes

1 reference

12 December 2020

The catalytic diversity of RNAs

1 reference

12 December 2020

Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid

1 reference

12 December 2020

Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid

1 reference

12 December 2020

Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme

1 reference

12 December 2020

The hammerhead cleavage reaction in monovalent cations

1 reference

12 December 2020

Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry

1 reference

12 December 2020

Dynamics and Metal Exchange Properties of C4C4 RING Domains from CNOT4 and the p44 Subunit of TFIIH

1 reference

12 December 2020

Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity

1 reference

12 December 2020

Three conserved guanosines approach the reaction site in native and minimal hammerhead ribozymes.

1 reference

12 December 2020

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

1 reference

12 December 2020

Two-metal-ion mechanism for hammerhead-ribozyme catalysis

1 reference

12 December 2020

Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets

1 reference

12 December 2020

Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

1 reference

12 December 2020

Tertiary contacts distant from the active site prime a ribozyme for catalysis

1 reference

12 December 2020

A conformational switch controls hepatitis delta virus ribozyme catalysis

1 reference

12 December 2020

Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.

1 reference

12 December 2020

Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme

1 reference

12 December 2020

Theoretical examination of two opposite mechanisms proposed for hepatitis delta virus ribozyme

1 reference

12 December 2020

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

1 reference

12 December 2020

Rfam: updates to the RNA families database

1 reference

12 December 2020

How enzymes work: analysis by modern rate theory and computer simulations

1 reference

12 December 2020

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

1 reference

12 December 2020

Two decades of RNA catalysis

1 reference

12 December 2020

Metal ion binding to catalytic RNA molecules

1 reference

12 December 2020

The tertiary structure of group II introns: implications for biological function and evolution

1 reference

12 December 2020

Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding

1 reference

12 December 2020

When to believe what you see.

1 reference

12 December 2020

The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme

1 reference

12 December 2020

Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations

1 reference

12 December 2020

Nucleobase catalysis in ribozyme mechanism

1 reference

12 December 2020

Autolytic processing of dimeric plant virus satellite RNA

1 reference

12 December 2020

Theoretical examination of Mg(2+)-mediated hydrolysis of a phosphodiester linkage as proposed for the hammerhead ribozyme

1 reference

12 December 2020

Crystal structure of a self-splicing group I intron with both exons

1 reference

12 December 2020

10.3390/MOLECULES15085389

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

13 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6257768&resulttype=core&format=json

13 May 2020

PubMed publication ID

20714304

1 reference