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Related Concept Videos

Ribozymes02:47

Ribozymes

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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...
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Introduction to Mechanisms of Enzyme Catalysis01:13

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For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
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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.
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Enzymes02:34

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Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
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Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.

Daniel Krochmal1, Yaming Shao1, Nan-Sheng Li1

  • 1Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.

Nature Chemical Biology
|January 21, 2022
PubMed
Summary
This summary is machine-generated.

This study reveals the high-resolution crystal structures of a self-alkylating ribozyme, detailing its hairpin-like architecture and how it binds epoxide substrates for RNA modification. These findings advance the development of novel chemical biology tools.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Chemical Biology

Background:

  • Ribozymes reacting with small molecules are vital for transcriptomics and chemical biology, enabling RNA labeling and imaging.
  • Understanding the structural basis of these RNA-modifying ribozymes is crucial for developing advanced RNA study tools.
  • High-resolution structures and catalytic mechanisms for this ribozyme class are currently limited.

Purpose of the Study:

  • To elucidate the structural basis and catalytic mechanism of a self-alkylating ribozyme.
  • To enable the development of improved RNA-modifying tools through structural insights.

Main Methods:

  • X-ray crystallography was used to determine the structures of the self-alkylating ribozyme in both apo and alkylated forms.
  • The structures were resolved at high resolutions of 1.71 Å (alkylated) and 2.49 Å (apo).
  • Kinetic studies involving substrate analogs and pH dependence were performed.

Main Results:

  • The crystal structures revealed an elongated, hairpin-like architecture of the ribozyme.
  • The ribozyme's structure is preorganized to bind the epoxide substrate in a specific hook-shaped conformation.
  • Reactivity studies and pH dependence suggest a requirement for epoxide protonation, potentially aided by substrate ether oxygens.

Conclusions:

  • The determined structures provide unprecedented insight into the architecture of self-alkylating ribozymes.
  • The findings offer a structural foundation for understanding the catalytic mechanism of nitrogen-carbon bond formation.
  • This work paves the way for designing more effective ribozyme-based tools for RNA research.