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Related Concept Videos

Enzymes02:34

Enzymes

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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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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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Induced-fit Model01:13

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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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Introduction to Enzymes01:22

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The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
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Catalytically Perfect Enzymes01:07

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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.
 
Most enzymes...
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Allosteric Proteins-ATCase01:19

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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.
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...
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The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities.

Ioannis G Riziotis1, António J M Ribeiro1, Neera Borkakoti1

  • 1European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD Cambridge, UK.

Journal of Molecular Biology
|August 31, 2023
PubMed
Summary

Enzymes utilize recurring catalytic residue arrangements called "modules of enzyme catalysis." These modules, identified using the Mechanism and Catalytic Site Atlas (M-CSA), aid in binding and catalysis, often arising from convergent evolution.

Keywords:
catalysiscatalytic residuesenzymemodulesstructure

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Enzyme catalysis relies on a limited set of residues and co-factors.
  • Recurring, structurally similar catalytic residue arrangements are expected across diverse enzymes.

Purpose of the Study:

  • To identify and characterize recurring catalytic motifs in enzymes.
  • To define these motifs as "modules of enzyme catalysis" and analyze their evolutionary origins and functions.

Main Methods:

  • Utilized the Mechanism and Catalytic Site Atlas (M-CSA) integrating enzyme structure, sequence, and mechanistic data.
  • Derived 3D templates representing catalytic residue groups.
  • Employed a fuzzy template-template search to identify recurring motifs.

Main Results:

  • Identified numerous "modules of enzyme catalysis" conserved or convergent across unrelated enzymes.
  • Found that many modules facilitate binding of metal ions, co-factors, and substrates, often through convergent evolution.
  • Observed that some convergent modules perform specific catalytic roles, like catalytic triads and saccharide-cleaving triads.
  • Demonstrated that enzyme active sites retain conserved modules even after functional divergence.

Conclusions:

  • A comprehensive library of catalytic modules has been compiled, characterizing a wide range of enzymes.
  • These modules serve as valuable templates for enzyme design and advancing the understanding of 3D enzyme catalysis.