Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

Riboswitches

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...

Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

Ribozymes

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...

Ribozymes

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...

Viruses with RNA Genomes

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells.

Nature communications·2026

Same author

VaWRKY26 transcription factor from Vitis amurensis negatively regulates plant cold tolerance.

Planta·2026

Same author

Structure basis for single-strand nucleic acid targeting by IscB and variants.

Nucleic acids research·2026

Same author

Suppression of host salicylic acid defense by a phloem-colonizing pathogen effector in citrus Huanglongbing.

Cell host & microbe·2026

Same author

Antitumor Immunity Mediated by Nanoreactors Based on Bacterial Membrane Vesicles.

Molecular pharmaceutics·2026

Same author

The rise of flexible perovskite tandem solar cells: configurations, progress, challenges, and future frontiers.

Chemical communications (Cambridge, England)·2026

Search research articles

Related Experiment Video

Updated: Jul 4, 2026

A Protocol for Analyzing Hepatitis C Virus Replication

A Protocol for Analyzing Hepatitis C Virus Replication

Published on: June 26, 2014

A conformational switch controls hepatitis delta virus ribozyme catalysis.

Ailong Ke¹, Kaihong Zhou, Fang Ding

¹Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94705, USA.

|May 14, 2004

Summary

Hepatitis delta virus (HDV) ribozymes use cytidine to activate a nucleophile for RNA cleavage. Structural analysis reveals RNA rearrangements and metal ion ejection post-cleavage, impacting catalytic activity.

More Related Videos

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System

Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System

Published on: December 21, 2019

Related Experiment Videos

Last Updated: Jul 4, 2026

A Protocol for Analyzing Hepatitis C Virus Replication

A Protocol for Analyzing Hepatitis C Virus Replication

Published on: June 26, 2014

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System

Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System

Published on: December 21, 2019

Area of Science:

Biochemistry
Molecular Biology
Structural Biology

Background:

Ribozymes, like protein enzymes, catalyze reactions.
The hepatitis delta virus (HDV) ribozyme cleaves RNA using divalent cations and cytidine.
Proposed mechanisms include general acid-base catalysis, substrate destabilization, and conformational changes.

Purpose of the Study:

To elucidate the catalytic mechanism of the HDV ribozyme.
To investigate the role of cytidine in RNA cleavage.
To understand the structural dynamics of the ribozyme before and after self-cleavage.

Main Methods:

X-ray crystallography
Analysis of ten crystal structures of the pre-cleaved HDV ribozyme.
Comparison of pre- and post-cleavage ribozyme structures.

Main Results:

Cytidine is positioned to activate the 2'-OH nucleophile in the precursor state, supporting its role as a general base.
Significant RNA conformational changes occur after cleavage.
A catalytically important divalent metal ion is ejected from the active site post-cleavage.

Conclusions:

RNA structural rearrangements are crucial for ribozyme and ribonucleoprotein enzyme activity.
The HDV ribozyme shares mechanistic similarities with protein ribonucleases and zymogens.
Conformational dynamics play an integral role in the biological activity of these enzymes.