Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P. (Q34364582)

1 August 2017

title

Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P. (English)

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1 August 2017

Bacillus subtilis

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Carol A Fierke

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1 August 2017

Sharon M Crary

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1 August 2017

Jeffrey C Kurz

series ordinal

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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

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1 August 2017

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1 August 2017

page(s)

933-947

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Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA.

1 August 2017

cites work

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Ribonuclease P: a ribonucleoprotein enzyme

6 July 2018

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Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA

6 July 2018

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The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited

6 July 2018

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An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction

6 July 2018

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Phosphorothioate substitution can substantially alter RNA conformation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Helix P4 is a divalent metal ion binding site in the conserved core of the ribonuclease P 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=1370310

Active site constraints in the hydrolysis reaction catalyzed by bacterial RNase P: analysis of precursor tRNAs with a single 3'-S-phosphorothiolate internucleotide linkage

6 July 2018

1 reference

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Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain

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

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On the role of magnesium ions in RNA stability

6 July 2018

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Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Ribonuclease P: unity and diversity in a tRNA processing 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=1370310

The protein component of Bacillus subtilis ribonuclease P increases catalytic efficiency by enhancing interactions with the 5' leader sequence of pre-tRNAAsp

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Expression, purification and characterization of the recombinant ribonuclease P protein component from Bacillus subtilis

6 July 2018

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Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates

6 July 2018

1 reference

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In vitro selection for altered divalent metal specificity in the RNase P RNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

A second catalytic metal ion in 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=1370310

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Ribonuclease P catalysis requires Mg2+ coordinated to the pro-RP oxygen of the scissile bond.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

In vitro selection of RNase P RNA reveals optimized catalytic activity in a highly conserved structural domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Metal-binding sites in the major groove of a large ribozyme domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Ribonuclease P (RNase P) RNA is converted to a Cd(2+)-ribozyme by a single Rp-phosphorothioate modification in the precursor tRNA at the RNase P cleavage 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=1370310

RNase P--a 'Scarlet Pimpernel'.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

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=1370310

Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Chemically modified RNA: approaches and applications

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Rp-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Evolutionary perspective on the structure and function of ribonuclease P, a 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=1370310

Salt-nucleic acid interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Stability constants of magnesium and cadmium complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of magnesium-ATP and magnesium-ADP

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Enzyme-Catalyzed Phosphoryl Transfer Reactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Synthesis of small RNAs using T7 RNA polymerase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Nucleoside phosphorothioates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Interaction of Escherichia coli tRNA(Ser) with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioate-containing tRNA transcripts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Absolute configuration of the diastereomers of adenosine 5'-O-(1-thiotriphosphate): consequences for the stereochemistry of polymerization by DNA-dependent RNA polymerase from Escherichia coli

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Identification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Comparative photocross-linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Identification of the universally conserved core of ribonuclease P 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=1370310

Circularly Permuted tRNAs as Specific Photoaffinity Probes of Ribonuclease P RNA Structure

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370310

Identification of phosphates involved in catalysis by the ribozyme RNase P 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=1370310

Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe

27 October 2018

1 reference

12 December 2020

Significant change in the structure of a ribozyme upon introduction of a phosphorothioate linkage at P9: NMR reveals a conformational fluctuation in the core region of a hammerhead ribozyme

1 reference

12 December 2020

Impact of phosphorothioate substitutions on the thermodynamic stability of an RNA GAAA tetraloop: an unexpected stabilization

1 reference

12 December 2020

Ion dependence of the Bacillus subtilis RNase P reaction

1 reference

12 December 2020

Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme

1 reference

12 December 2020

Gap-scan deletion analysis of Bacillus subtilis RNase P RNA

1 reference

12 December 2020

Multiple magnesium ions in the ribonuclease P reaction mechanism

1 reference

12 December 2020

A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P

1 reference

12 December 2020

Transient kinetic approaches to enzyme mechanisms

1 reference

12 December 2020

Magnesium ions are required by Bacillus subtilis ribonuclease P RNA for both binding and cleaving precursor tRNAAsp

1 reference

12 December 2020

A magnesium ion core at the heart of a ribozyme domain

1 reference

12 December 2020

Protein component of Bacillus subtilis RNase P specifically enhances the affinity for precursor-tRNAAsp

1 reference

12 December 2020

Counterion condensation revisited

1 reference

12 December 2020

Identification of individual nucleotides in the bacterial ribonuclease P ribozyme adjacent to the pre-tRNA cleavage site by short-range photo-cross-linking

1 reference

12 December 2020

A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution

1 reference

12 December 2020

Role of metal ions in the hydrolysis reaction catalyzed by RNase P RNA from Bacillus subtilis

1 reference

12 December 2020

Activities and relative affinities of divalent metals in unmodified and phosphorothioate-substituted hammerhead ribozymes

1 reference

12 December 2020

10.1017/S1355838202025025

Identifiers

DOI

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1 August 2017

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1 August 2017

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