Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Enzymes02:34

Enzymes

81.0K
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.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
81.0K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.7K
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.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
Enolate Mechanism Conventions01:15

Enolate Mechanism Conventions

2.1K
When a carbonyl compound is treated with a strong base, the α position gets deprotonated to give a resonance-stabilized intermediate called an enolate. Enolates are ambident nucleophiles because they possess two nucleophilic sites that can attack an electrophile owing to the delocalization of the negative charge between the α carbon and oxygen atoms. When the oxygen atom attacks an electrophile, it is called O-attack, whereas electrophilic attack via the α carbon is known as...
2.1K
Induced-fit Model01:13

Induced-fit Model

80.5K
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.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
80.5K
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

8.0K
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...
8.0K

You might also read

Related Articles

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

Sort by
Same author

Hopping-Type Charge Transport in Controllably p-Doped Polaronic Two-Dimensional Polymers.

Angewandte Chemie (International ed. in English)·2025
Same author

Gallic Acid-Encapsulated PAMAM Dendrimers as an Antioxidant Delivery System for Controlled Release and Reduced Cytotoxicity against ARPE-19 Cells.

Bioconjugate chemistry·2024
Same author

On the modeling of amplitude-sensitive electron spin resonance (ESR) detection using voltage-controlled oscillator (VCO)-based ESR-on-a-chip detectors.

Magnetic resonance (Gottingen, Germany)·2023
Same author

Elucidating the Origin of Plasmon-Generated Hot Holes in Water Oxidation.

ACS nano·2023
Same author

Coaxially Conductive Organic Wires Through Self-Assembly.

Journal of the American Chemical Society·2023
Same author

Advances in synthesis: general discussion.

Faraday discussions·2022

Related Experiment Video

Updated: Jun 11, 2025

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition
08:31

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition

Published on: October 3, 2018

8.4K

Bidentate Substrate Binding Mode in Oxalate Decarboxylase.

Alvaro Montoya1, Megan Wisniewski1, Justin L Goodsell1

  • 1Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611, USA.

Molecules (Basel, Switzerland)
|September 28, 2024
PubMed
Summary
This summary is machine-generated.

This study reveals that oxalate decarboxylase binds oxalate bidentate, not monodentate, challenging previous models. This finding impacts our understanding of enzyme mechanisms involving manganese and dioxygen.

Keywords:
ENDORbidentate coordinationoxalate decarboxylasesubstrate binding

More Related Videos

Expression, Purification, Crystallization, and Enzyme Assays of Fumarylacetoacetate Hydrolase Domain-Containing Proteins
10:21

Expression, Purification, Crystallization, and Enzyme Assays of Fumarylacetoacetate Hydrolase Domain-Containing Proteins

Published on: June 20, 2019

24.0K
Benchtop Immobilized Metal Affinity Chromatography, Reconstitution and Assay of a Polyhistidine Tagged Metalloenzyme for the Undergraduate Laboratory
08:02

Benchtop Immobilized Metal Affinity Chromatography, Reconstitution and Assay of a Polyhistidine Tagged Metalloenzyme for the Undergraduate Laboratory

Published on: August 23, 2018

17.4K

Related Experiment Videos

Last Updated: Jun 11, 2025

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition
08:31

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition

Published on: October 3, 2018

8.4K
Expression, Purification, Crystallization, and Enzyme Assays of Fumarylacetoacetate Hydrolase Domain-Containing Proteins
10:21

Expression, Purification, Crystallization, and Enzyme Assays of Fumarylacetoacetate Hydrolase Domain-Containing Proteins

Published on: June 20, 2019

24.0K
Benchtop Immobilized Metal Affinity Chromatography, Reconstitution and Assay of a Polyhistidine Tagged Metalloenzyme for the Undergraduate Laboratory
08:02

Benchtop Immobilized Metal Affinity Chromatography, Reconstitution and Assay of a Polyhistidine Tagged Metalloenzyme for the Undergraduate Laboratory

Published on: August 23, 2018

17.4K

Area of Science:

  • Biochemistry
  • Enzyme kinetics
  • Bioinorganic chemistry

Background:

  • Oxalate decarboxylase (EC 4.1.1.2) is an Mn- and O2-dependent enzyme crucial for oxalate metabolism.
  • Existing models propose monodentate substrate binding to facilitate dioxygen access, despite oxalate's preference for bidentate coordination.

Purpose of the Study:

  • To investigate the substrate binding mode of oxalate decarboxylase using experimental and computational methods.
  • To revise mechanistic hypotheses regarding substrate binding and dioxygen interaction in oxalate decarboxylase.

Main Methods:

  • X-band 13C-electron nuclear double resonance (ENDOR) spectroscopy on 13C-labeled oxalate.
  • Domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) calculations.
  • Density functional theory (DFT) geometry optimization of active site models.

Main Results:

  • ENDOR experiments demonstrate bidentate (κO, κO') binding of oxalate to the active site Mn(II) ion across different conditions and enzyme variants.
  • Computational methods predict ENDOR spectra consistent with bidentate binding and show it is energetically favored over monodentate binding.
  • The energetically preferred bidentate binding reconciles experimental data and challenges prior assumptions about dioxygen binding.

Conclusions:

  • Oxalate decarboxylase binds its substrate, oxalate, in a bidentate fashion to the active site Mn(II) ion.
  • This finding necessitates a revision of existing mechanistic models, particularly concerning the role and binding site of dioxygen.
  • The results support a revised mechanism involving long-range electron transfer for substrate activation.