The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis (Q35804539)

10 August 2017

The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis (English)

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10 August 2017

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Jana Sefcikova

1

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10 August 2017

Maryna V Krasovska

series ordinal

2

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10 August 2017

Jirí Sponer

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3

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10 August 2017

Nils G Walter

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4

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10 August 2017

language of work or name

English

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publication date

2 March 2007

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10 August 2017

Nucleic Acids Research

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10 August 2017

35

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10 August 2017

6

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10 August 2017

1933-1946

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describes a project that uses

10 August 2017

ImageQuant

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11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC1874588/fullTextXML

inferred from PubMed Central ID database lookup

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Trapped water molecules are essential to structural dynamics and function of a ribozyme

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

11 July 2018

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Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

11 July 2018

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Ribozyme catalysis: not different, just worse

11 July 2018

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11 July 2018

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On the occurrence of the T-loop RNA folding motif in large RNA molecules

11 July 2018

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Catalytic strategies of the hepatitis delta virus ribozymes

11 July 2018

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pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping

11 July 2018

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Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus

11 July 2018

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

11 July 2018

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Energetic contribution of non-essential 5' sequence to catalysis in a hepatitis delta virus ribozyme

11 July 2018

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Kinetic scheme for intermolecular RNA cleavage by a ribozyme derived from hepatitis delta virus RNA.

11 July 2018

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

11 July 2018

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A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes

11 July 2018

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HIV-1 A-rich RNA loop mimics the tRNA anticodon structure

11 July 2018

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Crystal structure of a hepatitis delta virus ribozyme

11 July 2018

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

11 July 2018

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Detailed analysis of base preferences at the cleavage site of a trans-acting HDV ribozyme: a mutation that changes cleavage site specificity

11 July 2018

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11 July 2018

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Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage

11 July 2018

1 reference

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Mutagenesis analysis of a hepatitis delta virus genomic ribozyme

11 July 2018

1 reference

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Three-dimensional structure of a hammerhead ribozyme

11 July 2018

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11 July 2018

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

11 July 2018

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Reversible cleavage and ligation of hepatitis delta virus RNA.

11 July 2018

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Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage.

11 July 2018

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The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant

11 July 2018

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Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

11 July 2018

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Sequence and structure of the catalytic RNA of hepatitis delta virus genomic RNA

11 July 2018

1 reference

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Random mutations to evaluate the role of bases at two important single-stranded regions of genomic HDV ribozyme

11 July 2018

1 reference

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Structural domains of transfer RNA molecules

11 July 2018

1 reference

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General acid catalysis by the hepatitis delta virus ribozyme

11 July 2018

1 reference

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Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

A conformational switch controls hepatitis delta virus ribozyme catalysis

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

Probing non-selective cation binding in the hairpin ribozyme with Tb(III).

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

GNRA tetraloops make a U-turn

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1874588

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

25 September 2018

1 reference

12 December 2020

Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change

1 reference

12 December 2020

Lanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes

1 reference

12 December 2020

Nucleotides -1 to -4 of hepatitis delta ribozyme substrate increase the specificity of ribozyme cleavage

1 reference

12 December 2020

A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKL1104

1 reference

10 August 2017

1 reference

10 August 2017

PubMed publication ID

17337436

1 reference