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Ribozyme structures and mechanisms

scientific article (publication date: 2001)

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title

Ribozyme structures and mechanisms (English)

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J A Doudna

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author name string

E A Doherty

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1

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language of work or name

English

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publication date

2001

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Annual Review of Biophysics and Biomolecular Structure

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30

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page(s)

457-75

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cites work

A kinetic and thermodynamic framework for the hammerhead ribozyme reaction

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

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A small catalytic oligoribonucleotide

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

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Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA

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

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A general two-metal-ion mechanism for catalytic RNA

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A self-splicing RNA excises an intron lariat

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Crystal structure of a conserved ribosomal protein-RNA complex

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Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

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A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate

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

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A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor

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

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An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis

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In vitro evolution of a self-alkylatlng ribozyme

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A Replication Cycle for Viroids and Other Small Infectious RNA's

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

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Site-specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions

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Ribonuclease P: unity and diversity in a tRNA processing ribozyme

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The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core

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Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron

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Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme

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Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement

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RNA folds: insights from recent crystal structures

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Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA

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RNA tectonics: towards RNA design

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Group II introns: elaborate ribozymes

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An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site

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

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Ionic interactions and the global conformations of the hammerhead ribozyme

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Defining the inside and outside of a catalytic RNA molecule

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Properties of an in vitro selected Pb2+ cleavage motif

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Solution structure of the loop B domain from the hairpin ribozyme

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The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of tetrahymena

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Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration

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Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes

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RNA conformational requirements of self-cleavage of hepatitis delta virus RNA

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A second catalytic metal ion in a group I ribozyme

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Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction

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The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme

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The three-dimensional structure of the ribosome and its components

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

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Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite

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A magnesium ion core at the heart of a ribozyme domain

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Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism

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Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis

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

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RNA-catalysed carbon–carbon bond formation

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Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions

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

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Folding of the HDV antigenomic ribozyme pseudoknot structure deduced from long-range photocrosslinks

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Inter-domain cross-linking and molecular modelling of the hairpin ribozyme

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The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme

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A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage

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Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes

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A re-investigation of the thio effect at the hammerhead cleavage site

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Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome

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Simple RNA enzymes with new and highly specific endoribonuclease activities

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Folding of group I introns from bacteriophage T4 involves internalization of the catalytic core

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Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding

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The solvent-protected core of the hairpin ribozyme-substrate complex

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9 October 2022

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Sequences required for self-catalysed cleavage of the satellite RNA of tobacco ringspot virus

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Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid

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Tertiary Structure Around the Guanosine-Binding Site of the Tetrahymena Ribozyme

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Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism

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

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

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9 October 2022

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Peptide bond formation by in vitro selected ribozymes

1 reference

9 October 2022

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Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme

1 reference

9 October 2022

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RNA catalytic properties of the minimum (-)sTRSV sequence

1 reference

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

1 reference

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Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5' splice site domain

1 reference

9 October 2022

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

1 reference

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Role of divalent metal ions in the hammerhead RNA cleavage reaction

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A small metalloribozyme with a two-step mechanism

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Tertiary Motifs in RNA Structure and Folding

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Order, dynamics and metal-binding in the lead-dependent ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A minor groove RNA triple helix within the catalytic core of a group I intron

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Structure and activities of group II introns

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

The Structural Basis of Hammerhead Ribozyme Self-Cleavage

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

X-ray crystal structures of 70S ribosome functional complexes

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Autolytic processing of dimeric plant virus satellite RNA

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Metal ion catalysis in the Tetrahymena ribozyme reaction

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A crystallographic study of metal-binding to yeast phenylalanine transfer RNA

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Three-dimensional structure of a hammerhead ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5.

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Metal Ions Play a Passive Role in the Hairpin Ribozyme Catalysed Reaction

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Aminoacyl-RNA synthesis catalyzed by an RNA.

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

The guanosine binding site of the Tetrahymena ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Self-splicing of group I introns

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Role of Nd3+ and Pb2+ on the RNA cleavage reaction by a small ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Human hepatitis delta virus RNA subfragments contain an autocleavage activity

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Ribozymes: A Distinct Class of Metalloenzymes

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Identification of phosphate oxygens that are important for self-cleavage activity of the HDV ribozyme by phosphorothioate substitution interference analysis

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Sequential Folding of the Genomic Ribozyme of the Hepatitis Delta Virus: Structural Analysis of RNA Transcription Intermediates

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A detailed view of a ribosomal active site: the structure of the L11-RNA complex

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Inhibition of the Hammerhead Ribozyme Cleavage Reaction by Site-Specific Binding of Tb(III)

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Movement of the Guide Sequence During RNA Catalysis by a Group I Ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

In vitro selection of RNAs that undergo autolytic cleavage with Pb2+

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Evolutionary variation in bacterial RNase P RNAs

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation.

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Crystal structure of a hepatitis delta virus ribozyme

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

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

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Comparative and functional anatomy of group II catalytic introns—a review

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

An AU at the first base pair of helix 3 elevates the catalytic activity of hepatitis delta virus ribozymes

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Reconstitution of a group I intron self-splicing reaction with an activator RNA.

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Ribozyme-catalysed amino-acid transfer reactions

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements

1 reference

9 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

A Detailed View of a Ribosomal Active Site

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1146/ANNUREV.BIOPHYS.30.1.457

Identifiers

DOI

10.1146/ANNUREV.BIOPHYS.30.1.457

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

4371994

Fatcat ID

release_2ih4rqypyjdwfcgjcjet77qlse

1 reference

stated in

Fatcat

reference URL

https://api.fatcat.wiki/v0/release/2ih4rqypyjdwfcgjcjet77qlse

retrieved

24 November 2022

based on heuristic

mapped directly with Wikidata item

OpenCitations bibliographic resource ID

4371994

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

4371994

PubMed publication ID

11441810

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

4371994

ResearchGate publication ID

11899091

0 references

(Q28205184)

Ribozyme structures and mechanisms

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