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

The Phosphorus Cycle01:21

The Phosphorus Cycle

Unlike carbon, water, and nitrogen, phosphorus is not present in the atmosphere as a gas. Instead, most phosphorus in the ecosystem exists as compounds, such as phosphate ions (PO43-), found in soil, water, sediment and rocks. Phosphorus is often a limiting nutrient (i.e., in short supply). Consequently, phosphorus is added to most agricultural fertilizers, which can cause environmental problems related to runoff in aquatic ecosystems.
Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Phosphoinositides and PIPs01:42

Phosphoinositides and PIPs

Phosphoinositides are a group of phospholipids containing a glycerol backbone with two fatty acid chains and a phosphate attached to a myoinositol sugar ring. The inositol head group extends into the cytoplasm, where it is modified by adding phosphate groups to form phosphatidylinositol phosphates or PIPs.
Different phosphoinositides are synthesized and recruited on the cytosolic face of the plasma membrane. The localization of specific phosphoinositides concentrated in separate membrane...
Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Environmental Applications of Microorganisms01:30

Environmental Applications of Microorganisms

Microorganisms play a pivotal role in maintaining ecosystem balance by recycling essential elements such as carbon, nitrogen, and phosphorus, as well as supporting processes like bioremediation, wastewater treatment, and biofuel production.Microbes in Elemental CyclesIn the carbon cycle, microorganisms decompose organic matter, releasing carbon dioxide via aerobic respiration. This carbon dioxide is subsequently used by photosynthetic organisms to synthesize organic compounds, closing the...
Bioplastics01:27

Bioplastics

Bioplastics derived from microbial processes present a sustainable alternative to conventional petroleum-based plastics. Among these, polyhydroxyalkanoates (PHAs), particularly polyhydroxybutyrates (PHBs), have emerged as prominent candidates due to their biodegradability and biocompatibility. These polymers are synthesized by a variety of bacteria, such as Cupriavidus necator and Pseudomonas putida, which naturally accumulate PHAs as intracellular carbon and energy reserves, especially under...

You might also read

Related Articles

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

Sort by
Same author

Molecular basis of specificity and deamidation of eIF4A by Burkholderia Lethal Factor 1.

Communications biology·2022
Same author

Evolution of catalytic centers of antibodies by virtual screening of broad repertoire of mutants using supercomputer.

Doklady. Biochemistry and biophysics·2017
Same author

An arginase-1 SNP that protects against the development of pulmonary hypertension in bronchopulmonary dysplasia enhances NO-mediated apoptosis in lymphocytes.

Physiological reports·2016
Same author

Nitric oxide-donating derivatives of hederacolchiside A<sub>1</sub>: Synthesis and biological evaluation in vitro and in vivo as potential anticancer agents.

Bioorganic & medicinal chemistry letters·2016
Same author

Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes.

Angewandte Chemie (International ed. in English)·2016
Same author

Comparative Analysis of the Effects of Hydroxysafflor Yellow A and Anhydrosafflor Yellow B in Safflower Series of Herb Pairs Using Prep-HPLC and a Selective Knock-Out Approach.

Molecules (Basel, Switzerland)·2016

Related Experiment Video

Updated: May 16, 2026

Immobilization of Multi-biocatalysts in Alginate Beads for Cofactor Regeneration and Improved Reusability
09:27

Immobilization of Multi-biocatalysts in Alginate Beads for Cofactor Regeneration and Improved Reusability

Published on: April 22, 2016

Reflections on biocatalysis involving phosphorus.

G M Blackburn1, M W Bowler, Yi Jin

  • 1Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK. g.m.blackburn@shef.ac.uk

Biochemistry. Biokhimiia
|November 20, 2012
PubMed
Summary

Metal fluorides, like trifluoromagnesate, serve as crucial transition state analogues for studying enzyme mechanisms. These mimics reveal insights into phosphoryl group transfer, aiding our understanding of enzyme catalysis.

More Related Videos

Defining Substrate Specificities for Lipase and Phospholipase Candidates
08:59

Defining Substrate Specificities for Lipase and Phospholipase Candidates

Published on: November 23, 2016

Related Experiment Videos

Last Updated: May 16, 2026

Immobilization of Multi-biocatalysts in Alginate Beads for Cofactor Regeneration and Improved Reusability
09:27

Immobilization of Multi-biocatalysts in Alginate Beads for Cofactor Regeneration and Improved Reusability

Published on: April 22, 2016

Defining Substrate Specificities for Lipase and Phospholipase Candidates
08:59

Defining Substrate Specificities for Lipase and Phospholipase Candidates

Published on: November 23, 2016

Area of Science:

  • Biochemistry and Structural Biology
  • Enzyme Catalysis and Mechanism
  • Bioinorganic Chemistry

Background:

  • Early research focused on phosphonates as phosphate analogues, progressing to structural studies with nucleotide-utilising enzymes.
  • Metal fluorides emerged as effective analogues for the phosphoryl group, enabling transition state analysis in enzyme reactions.

Purpose of the Study:

  • To review the characteristics of enzyme transition state analogues (TSA) for various reactions.
  • To highlight the utility of trifluoromagnesate (MgF3-) as an ideal TSA for phosphoryl transfer, providing trigonal bipyramidal geometry.
  • To elucidate the mechanism of phosphoryl group transfer in enzymes using structural and mechanistic insights.

Main Methods:

  • Utilisation of metal fluoride species, including trifluoroberyllate, tetrafluoroaluminate, and trifluoromagnesate, as transition state analogues.
  • Application of fluorine-19 Nuclear Magnetic Resonance ((19)F NMR) and protein crystallography for structural studies.
  • Analysis of ground state (GS) and transition state (TS) structures, including near-attack conformers.

Main Results:

  • Trifluoroberyllate mimics ground states with tetrahedral geometry, while tetrafluoroaluminate imposes octahedral geometry, unsuitable for phosphoryl transfer.
  • Trifluoromagnesate (MgF3-) successfully provides the required trigonal bipyramidal (tbp) geometry and anionic charge for transition state mimicry.
  • Redefinition of several reported tbp structures previously assigned as AlF3 cores to MgF3 complexes.
  • Structural data support charge balance in transition states and concerted-associative pathways for biocatalysis.
  • Superposition of GS and TS structures reveals phosphorus migration through a near-stationary equatorial oxygen triangle during associative phosphoryl transfer.

Conclusions:

  • Trifluoromagnesate is a superior transition state analogue for studying phosphoryl transfer enzymes due to its appropriate geometry and charge.
  • Structural insights into transition states and near-attack conformers significantly advance the understanding of enzyme catalysis.
  • The findings support a detailed mechanistic description of phosphoryl group transfer, emphasizing charge balance and associative pathways.