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Related Concept Videos

Ribozymes02:47

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...
Ribozymes02:47

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...
Cofactors and Coenzymes01:27

Cofactors and Coenzymes

Enzymes require additional components for proper function. There are two such classes of molecules: cofactors and coenzymes. Cofactors are metallic ions and coenzymes are non-protein organic molecules. Both of these types of helper molecule can be tightly bound to the enzyme or bound only when the substrate binds.
Cofactors and Coenzymes01:24

Cofactors and Coenzymes

Enzymes are proteins made of amino acids. The functional group of each constituent amino acid catalyzes a wide variety of chemical reactions via ionic interactions or acid-base reactions. However, amino acids cannot catalyze oxidation-reduction and group transfer reactions and need to be aided by non-protein components called cofactors. Cofactors are also referred to as the chemical teeth of an enzyme.
Cofactors can be metallic ions or organic molecules called coenzymes. These types of helper...
Cofactors and Coenzymes01:27

Cofactors and Coenzymes

Enzymes require additional components for proper function. There are two such classes of molecules: cofactors and coenzymes. Cofactors are metallic ions and coenzymes are non-protein organic molecules. Both of these types of helper molecule can be tightly bound to the enzyme or bound only when the substrate binds.
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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 a mild...

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An active-site guanine participates in glmS ribozyme catalysis in its protonated state.

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Related Experiment Video

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Preparation, Purification, and Use of Fatty Acid-containing Liposomes
10:43

Preparation, Purification, and Use of Fatty Acid-containing Liposomes

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The glmS ribozyme cofactor is a general acid-base catalyst.

Júlia Viladoms1, Martha J Fedor

  • 1Department of Chemical Physiology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Journal of the American Chemical Society
|November 2, 2012
PubMed
Summary
This summary is machine-generated.

The glmS ribozyme uses a d-glucosamine-6-phosphate (GlcN6P) cofactor. This study shows GlcN6P acts as a general acid catalyst, directly participating in the glmS ribozyme

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • RNA Catalysis

Background:

  • The glmS ribozyme is a unique self-cleaving RNA requiring a cofactor.
  • The precise catalytic role of the d-glucosamine-6-phosphate (GlcN6P) cofactor remains unclear.
  • Previous hypotheses suggested GlcN6P functions as a general acid.

Purpose of the Study:

  • To investigate the catalytic mechanism of the glmS ribozyme.
  • To determine the role of the GlcN6P cofactor in glmS ribozyme self-cleavage.
  • To establish whether GlcN6P acts as a general acid catalyst.

Main Methods:

  • Screening of GlcN6P-like molecules for glmS ribozyme self-cleavage activity.
  • Analysis of the pH dependence of the cleavage reaction.
  • Correlation of cofactor acidity with rate enhancement.
  • Determination of the Brønsted coefficient (β).

Main Results:

  • A strong correlation was observed between pH dependence and cofactor acidity.
  • Cofactor efficiency was proportional to intrinsic acidity for low-affinity binders.
  • A linear free-energy relationship supports a general acid-base catalysis mechanism.
  • A high Brønsted coefficient (β ~ 0.7) indicates significant proton transfer in the transition state.

Conclusions:

  • The GlcN6P cofactor directly participates in the glmS ribozyme catalytic mechanism.
  • The glmS ribozyme utilizes exogenous acid-base catalysis, a novel finding for self-cleaving RNAs.
  • This study elucidates the catalytic role of the GlcN6P cofactor in glmS ribozyme function.