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Related Concept Videos

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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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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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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Induced-fit Model01:13

Induced-fit Model

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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.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
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SN2 Reaction: Stereochemistry02:23

SN2 Reaction: Stereochemistry

12.3K
In an SN2 reaction, the nucleophilic attack on the substrate and departure of the leaving group occurs simultaneously through a transition state. As the nucleophile approaches the substrate from the back-side, the configuration of the substrate carbon changes from tetrahedral to trigonal bipyramidal and then back to tetrahedral, leading to an inversion in the configuration of the product.
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SN2 Reaction: Mechanism02:27

SN2 Reaction: Mechanism

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The kinetic studies of SN2 reactions suggest an essential feature of its mechanism: it is a single-step process without intermediates. Here, both the nucleophile and the substrate participate in the rate-determining step.
The presence of the more electronegative halogen in the substrate creates a polarized carbon-halide bond. The halide pulls the electron cloud generating an electrophilic center at the carbon atom. Thus, the carbon atom carries a partial positive charge while the halide has a...
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Substrate Generation for Endonucleases of CRISPR/Cas Systems
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Structural Insights into Substrate Recognition by Clostridium difficile Sortase.

Jui-Chieh Yin1, Chun-Hsien Fei1, Yen-Chen Lo2

  • 1Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University Tainan, Taiwan.

Frontiers in Cellular and Infection Microbiology
|December 7, 2016
PubMed
Summary
This summary is machine-generated.

Sortases attach surface proteins to bacterial cell walls. Researchers identified a specific amino acid interaction crucial for *Clostridium difficile* sortase B to recognize its peptide substrate, enabling targeted protein attachment.

Keywords:
Clostridium difficilecrystal structurefluorescence resonance energy transfersortasesubstrate specificity

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Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
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Area of Science:

  • Microbiology
  • Biochemistry
  • Structural Biology

Background:

  • Sortases are essential bacterial enzymes catalyzing surface protein anchoring to the cell wall.
  • Understanding sortase substrate specificity is key to bacterial virulence mechanisms.
  • Diverse bacterial species possess sortases with conserved structures but unclear specificity.

Purpose of the Study:

  • To elucidate the molecular basis of *Clostridium difficile* sortase B (Cd-SrtB) specific recognition of the PPKTG peptide substrate.
  • To investigate the role of specific amino acid residues in substrate binding and cleavage efficiency.

Main Methods:

  • Computational modeling of the Cd-SrtB-peptide complex.
  • Biochemical assays, including site-directed mutagenesis.
  • Fluorescence resonance energy transfer (FRET) assays for functional validation.

Main Results:

  • A computational model of the Cd-SrtBΔN26-PPKTG complex was successfully constructed and validated.
  • Specific interactions between Cd-SrtB and the fourth amino acid N-terminal to the cleavage site of PPKTG were identified.
  • This interaction is essential for orienting the peptide for efficient, substrate-specific cleavage.

Conclusions:

  • The study reveals a critical molecular interaction driving sortase substrate specificity.
  • This finding provides insights into the mechanism of sortase-mediated protein ligation in *Clostridium difficile*.
  • The identified interaction could be a target for future antimicrobial strategies.