(Q33776595)

English

Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data (English)

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

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author name string

Timothy J Wilson

1

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

David M J Lilley

2

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

language of work or name

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publication date

20 December 2010

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

17

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

2

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

213-221

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

The complete VS ribozyme in solution studied by small-angle X-ray scattering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Essential role of an active-site guanine in glmS ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

A guanine nucleobase important for catalysis by the VS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Active site labeling of G8 in the hairpin ribozyme: implications for structure and mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Nucleobase catalysis in the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Role of an active site adenine in hairpin ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Efficient, pH-dependent RNA ligation by the VS ribozyme in trans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Ionization of a Critical Adenosine Residue in theNeurosporaVarkud Satellite Ribozyme Active Site†

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Transition state stabilization by a catalytic RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

4-thio-U cross-linking identifies the active site of the VS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Metal ion binding and the folding of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

The global structure of the VS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Crystal structure of a hepatitis delta virus ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

A long-range pseudoknot is required for activity of the Neurospora VS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

RNA catalytic properties of the minimum (-)sTRSV sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

4 July 2018

Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

General acid catalysis by the hepatitis delta virus ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

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

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

Nucleobase participation in ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

A conformational switch controls hepatitis delta virus ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

Functional group requirements in the probable active site of the VS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

The A730 loop is an important component of the active site of the VS ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3022271

30 October 2018

Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/21173201

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Purine functional groups in essential residues of the hairpin ribozyme required for catalytic cleavage of RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/21173201

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mutational analysis of loops 1 and 5 of the hairpin ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/21173201

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops

1 reference

https://pubmed.ncbi.nlm.nih.gov/21173201

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions

1 reference

https://pubmed.ncbi.nlm.nih.gov/21173201

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Folding of the four-way RNA junction of the hairpin ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/21173201

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Observation of internal cleavage and ligation reactions of a ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/21173201

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1261/RNA.2473711

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

ResearchGate publication ID

0 references

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