Structure-function relationships in the hammerhead ribozyme probed by base rescue (Q43206329)

16 November 2017

Structure-function relationships in the hammerhead ribozyme probed by base rescue (English)

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16 November 2017

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A Peracchi

1

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author name string

J Matulic-Adamic

2

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16 November 2017

S Wang

3

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16 November 2017

L Beigelman

4

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16 November 2017

D Herschlag

5

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16 November 2017

language of work or name

English

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publication date

1 November 1998

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16 November 2017

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16 November 2017

4

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16 November 2017

11

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16 November 2017

1332-1346

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The structural basis of hammerhead ribozyme self-cleavage

16 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

1-Deazaadenosine: synthesis and activity of base-modified hammerhead ribozymes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Functional groups on the cleavage site pyrimidine nucleotide are required for stabilization of the hammerhead transition state

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

The structure, function and application of the hammerhead ribozyme

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

A test of the role of the proximal histidines in the Perutz model for cooperativity in haemoglobin

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Chemical rescue of Asp237-->Ala and Lys358-->Ala mutants in the lactose permease of Escherichia coli

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Structure and function of the hammerhead ribozyme: an unfinished story

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: implications for secondary structure

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Catalytic role of 2'-hydroxyl groups within a group II intron active site

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Lysine 87 in the beta subunit of tryptophan synthase that forms an internal aldimine with pyridoxal phosphate serves critical roles in transimination, catalysis, and product release

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Evidence for lysine 80 as general base catalyst of leucine dehydrogenase.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Replacement of the proximal ligand of sperm whale myoglobin with free imidazole in the mutant His-93-->Gly

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

A kinetic and thermodynamic framework for the hammerhead ribozyme reaction

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Three-dimensional structure of a hammerhead ribozyme

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Regeneration of catalytic activity of glutamine synthetase mutants by chemical activation: exploration of the role of arginines 339 and 359 in activity

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

RNA chaperones and the RNA folding problem

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Synthesis, deprotection, analysis and purification of RNA and ribozymes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

The hammerhead RNA domain, a model ribozyme

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

The roles of the conserved pyrimidine bases in hammerhead ribozyme catalysis: evidence for a magnesium ion-binding site

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Direct Brønsted analysis of the restoration of activity to a mutant enzyme by exogenous amines

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Remodeling hexose-1-phosphate uridylyltransferase: mechanism-inspired mutation into a new enzyme, UDP-hexose synthase

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Numbering system for the hammerhead

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Importance of specific purine amino and hydroxyl groups for efficient cleavage by a hammerhead ribozyme

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Brønsted analysis of aspartate aminotransferase via exogenous catalysis of reactions of an inactive mutant

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Guanidine derivatives restore activity to carboxypeptidase lacking arginine‐127

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

An Analysis of the Structure of tRNA

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Mutagenesis and chemical rescue indicate residues involved in beta-aspartyl-AMP formation by Escherichia coli asparagine synthetase B.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Chemical rescue by guanidine derivatives of an arginine-substituted site-directed mutant of Escherichia coli ornithine transcarbamylase.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Sequence requirements of the hammerhead RNA self-cleavage reaction

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Rescue of the catalytic activity of an H42A mutant of horseradish peroxidase by exogenous imidazoles

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Exogenous acetate reconstitutes the enzymatic activity of trypsin Asp189Ser

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Nucleoside modifications stabilize Mg2+ binding in Escherichia coli tRNA(Val): an imino proton NMR investigation.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Major contribution of a carboxymethyl group to transition-state stabilization by cytidine deaminase: mutation and rescue.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Effect of nucleoside modifications on the structure and thermal stability of Escherichia coli valine tRNA.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Chemical rescue by exogenous amines of a site-directed mutant of ribulose 1,5-bisphosphate carboxylase/oxygenase that lacks a key lysyl residue

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369707

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

3 November 2018

1 reference

12 December 2020

Structural feature of the initiator tRNA gene from Pyrodictium occultum and the thermal stability of its gene product, tRNA(imet)

1 reference

12 December 2020

Importance of specific adenosine N7-nitrogens for efficient cleavage by a hammerhead ribozyme. A model for magnesium binding

1 reference

12 December 2020

Transducin activation by rhodopsin without a covalent bond to the 11-cis-retinal chromophore

1 reference

12 December 2020

Effect of structural modifications on the activity of the leadzyme

1 reference

12 December 2020

Importance of specific adenosine N3-nitrogens for efficient cleavage by a hammerhead ribozyme

1 reference

12 December 2020

Synthesis and Structure of 1-Deoxy-1-phenyl-beta-D-ribofuranose and Its Incorporation into Oligonucleotides

1 reference

12 December 2020

Probing the mechanism and improving the rate of substrate-assisted catalysis in subtilisin BPN'

1 reference

12 December 2020

Importance of specific guanosine N7-nitrogens and purine amino groups for efficient cleavage by a hammerhead ribozyme

1 reference

12 December 2020

Isoguanosine substitution of conserved adenosines in the hammerhead ribozyme

1 reference

12 December 2020

The role of the exocyclic amino groups of conserved purines in hammerhead ribozyme cleavage

1 reference

12 December 2020

Identification and characterization of a catalytic base in bacterial luciferase by chemical rescue of a dark mutant

1 reference

12 December 2020

Demonstration of a functional requirement for the carbamate nitrogen of ribulosebisphosphate carboxylase/oxygenase by chemical rescue

1 reference

12 December 2020

Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism

1 reference

12 December 2020

Structure of an unmodified tRNA molecule

1 reference

12 December 2020

Effect of cytidine‐5′‐monophosphate on peptidyl transferase activity

1 reference

12 December 2020

10.1017/S1355838298980979

Identifiers

DOI

1 reference

16 November 2017

1 reference

16 November 2017

PubMed publication ID

9814755

1 reference