(Q36116084)

12 August 2017

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title

Ribozyme catalysis: not different, just worse (English)

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12 August 2017

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2

Jon R Lorsch

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Jennifer Doudna

series ordinal

1

object named as

Jennifer A Doudna

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12 August 2017

1 May 2005

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Nature Structural & Molecular Biology

12 August 2017

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12 August 2017

12

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12 August 2017

395-402

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12 August 2017

5

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https://scigraph.springernature.com/pub.10.1038/nsmb932

12 August 2017

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cites work

Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes

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Role of Entropy in Increased Rates of Intramolecular Reactions

21 January 2018

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Two-metal-Ion catalysis in adenylyl cyclase

21 January 2018

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Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin

21 January 2018

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Structural diversity of self-cleaving ribozymes

21 January 2018

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In vitro evolution suggests multiple origins for the hammerhead ribozyme

21 January 2018

1 reference

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

21 January 2018

1 reference

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements.

21 January 2018

1 reference

Hammerhead ribozyme kinetics

21 January 2018

1 reference

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

21 January 2018

1 reference

The hammerhead cleavage reaction in monovalent cations

21 January 2018

1 reference

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

21 January 2018

1 reference

Three-dimensional structure of a hammerhead ribozyme

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

The structural basis of hammerhead ribozyme self-cleavage

21 January 2018

1 reference

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

21 January 2018

1 reference

A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction

21 January 2018

1 reference

A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme

21 January 2018

1 reference

Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction

21 January 2018

1 reference

Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation.

21 January 2018

1 reference

A re-investigation of the thio effect at the hammerhead cleavage site

21 January 2018

1 reference

Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate

21 January 2018

1 reference

Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?

21 January 2018

1 reference

Crystal structure of a hepatitis delta virus ribozyme

21 January 2018

1 reference

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Triple-strand formation in the homopurine:homopyrimidine DNA oligonucleotides d(G-A)4 and d(T-C)4

21 January 2018

1 reference

Formation of a stable triplex from a single DNA strand

21 January 2018

1 reference

RNAs with dual specificity and dual RNAs with similar specificity

21 January 2018

1 reference

Adenine protonation in domain B of the hairpin ribozyme

21 January 2018

1 reference

Self-cleaving ribozymes of hepatitis delta virus RNA.

21 January 2018

1 reference

Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis

21 January 2018

1 reference

Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme

21 January 2018

1 reference

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

21 January 2018

1 reference

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

21 January 2018

1 reference

Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions.

21 January 2018

1 reference

Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme

21 January 2018

1 reference

A conformational switch controls hepatitis delta virus ribozyme catalysis

21 January 2018

1 reference

Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue

21 January 2018

1 reference

Transition state stabilization by a catalytic RNA

21 January 2018

1 reference

Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis

21 January 2018

1 reference

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

21 January 2018

1 reference

The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis

21 January 2018

1 reference

Modular engineering of a Group I intron ribozyme

21 January 2018

1 reference

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

21 January 2018

1 reference

A three-dimensional perspective on exon binding by a group II self-splicing intron

21 January 2018

1 reference

Visualizing the solvent-inaccessible core of a group II intron ribozyme

21 January 2018

1 reference

Structural insights into group II intron catalysis and branch-site selection

21 January 2018

1 reference

Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

21 January 2018

1 reference

Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site

21 January 2018

1 reference

Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site

21 January 2018

1 reference

Stereochemistry of RNA cleavage by the Tetrahymena ribozyme and evidence that the chemical step is not rate-limiting

21 January 2018

1 reference

Stereochemical course of catalysis by the Tetrahymena ribozyme

21 January 2018

1 reference

Three metal ions at the active site of the Tetrahymena group I ribozyme

21 January 2018

1 reference

Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2'-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme

21 January 2018

1 reference

Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction

21 January 2018

1 reference

Metal ion catalysis in the Tetrahymena ribozyme reaction

21 January 2018

1 reference

Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization

21 January 2018

1 reference

Crystal structure of a group I ribozyme domain: principles of RNA packing

21 January 2018

1 reference

A preorganized active site in the crystal structure of the Tetrahymena ribozyme

21 January 2018

1 reference

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

21 January 2018

1 reference

Crystal structure of a phage Twort group I ribozyme-product complex

21 January 2018

1 reference

A general two-metal-ion mechanism for catalytic RNA

21 January 2018

1 reference

Phosphorothioate modification of RNA for stereochemical and interference analyses

21 January 2018

1 reference

Initiation, elongation, and termination strategies in polyketide and polypeptide antibiotic biosynthesis

21 January 2018

1 reference

Learning from nature's drug factories: nonribosomal synthesis of macrocyclic peptides

21 January 2018

1 reference

Polyketide and nonribosomal peptide antibiotics: modularity and versatility

21 January 2018

1 reference

Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites

21 January 2018

1 reference

Unusual resistance of peptidyl transferase to protein extraction procedures

21 January 2018

1 reference

A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome

21 January 2018

1 reference

Mutations at nucleotides G2251 and U2585 of 23 S rRNA perturb the peptidyl transferase center of the ribosome

21 January 2018

1 reference

Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA.

21 January 2018

1 reference

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

21 January 2018

1 reference

The ribosome as an entropy trap

21 January 2018

1 reference

The structural basis of ribosome activity in peptide bond synthesis

21 January 2018

1 reference

Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome.

21 January 2018

1 reference

The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release.

21 January 2018

1 reference

Substrate-assisted catalysis of peptide bond formation by the ribosome

21 January 2018

1 reference

Control of gene expression by a natural metabolite-responsive ribozyme

21 January 2018

1 reference

Autocatalytic RNA cleavage in the human beta-globin pre-mRNA promotes transcription termination

21 January 2018

1 reference

Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity

21 January 2018

1 reference

Structures and mechanisms of Nudix hydrolases.

21 January 2018

1 reference

The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis,

21 January 2018

1 reference

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

21 January 2018

1 reference

Energetics of Catalysis by Ribonucleases: Fate of the 2',3'-Cyclic Phosphodiester Intermediate

21 January 2018

1 reference

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

21 January 2018

1 reference

Observation of internal cleavage and ligation reactions of a ribozyme

31 March 2020

1 reference

A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage

31 March 2020

1 reference

An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis

31 March 2020

1 reference

A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis

31 March 2020

1 reference

Steric interference modification of the hammerhead ribozyme

31 March 2020

1 reference

Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme

31 March 2020

1 reference

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

31 March 2020

1 reference

A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center

31 March 2020

1 reference

Escherichia coli ribosomes translate in vivo with variable rate

31 March 2020

1 reference

Construction and initial characterization of Escherichia coli strains with few or no intact chromosomal rRNA operons.

31 March 2020

1 reference

inferred from DOI database lookup

7 January 2021

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Identifiers

DOI

10.1038/NSMB932

1 reference

PubMed ID

15870731

Dimensions Publication ID

12 August 2017

0 references

1 reference

PubMed ID

15870731