Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis (Q34364540)

1 August 2017

title

Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis (English)

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1 August 2017

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Shu-ou Shan

1

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1 August 2017

Daniel Herschlag

series ordinal

2

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1 August 2017

language of work or name

English

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publication date

1 July 2002

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1 August 2017

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1 August 2017

volume

8

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1 August 2017

issue

7

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1 August 2017

page(s)

861-872

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Ribozyme structures and mechanisms

1 August 2017

cites work

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction

6 July 2018

1 reference

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme

6 July 2018

1 reference

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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

6 July 2018

1 reference

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Crystal structure of a hepatitis delta virus ribozyme

6 July 2018

1 reference

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Molecular movement inside the translational engine

6 July 2018

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Mechanical devices of the spliceosome: motors, clocks, springs, and things

6 July 2018

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Induced folding in RNA-protein recognition: more than a simple molecular handshake

6 July 2018

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Structure, recognition and adaptive binding in RNA aptamer complexes

6 July 2018

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Effects of Mg2+ and the 2' OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions

6 July 2018

1 reference

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A second catalytic metal ion in group I ribozyme

6 July 2018

1 reference

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

6 July 2018

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Multiple tertiary interactions involving domain II of group II self-splicing introns.

6 July 2018

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Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme

6 July 2018

1 reference

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

6 July 2018

1 reference

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Isolation of a local tertiary folding transition in the context of a globally folded RNA.

6 July 2018

1 reference

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Conformational switches involved in orchestrating the successive steps of group I RNA splicing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Metal ion catalysis in the Tetrahymena ribozyme reaction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding

6 July 2018

1 reference

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Oligonucleotide duplexes containing 2'-amino-2'-deoxycytidines: thermal stability and chemical reactivity

6 July 2018

1 reference

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Dissection of the role of the conserved G.U pair in group I RNA self-splicing

6 July 2018

1 reference

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Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5' cleavage site into a high free energy binding mode in the Tetrahymena ribozyme

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

A positive entropy change for guanosine binding and for the chemical step in the Tetrahymena ribozyme reaction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Ribozyme inhibitors: deoxyguanosine and dideoxyguanosine are competitive inhibitors of self-splicing of the Tetrahymena ribosomal ribonucleic acid precursor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Stereochemical course of catalysis by the Tetrahymena ribozyme

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Guanosine binding required for cyclization of the self-splicing intervening sequence ribonucleic acid from Tetrahymena thermophila

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370303

Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods

27 October 2018

1 reference

12 December 2020

Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site

1 reference

12 December 2020

Ribozyme crevices and catalysis

1 reference

12 December 2020

A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme

1 reference

12 December 2020

10.1017/S1355838202020216

Identifiers

DOI

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1 August 2017

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1 August 2017

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