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Related Concept Videos

Protein Modifications in the RER01:26

Protein Modifications in the RER

Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal sequences.
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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Related Experiment Video

Updated: May 20, 2026

In Vitro Analysis of E3 Ubiquitin Ligase Function
06:06

In Vitro Analysis of E3 Ubiquitin Ligase Function

Published on: May 14, 2021

E2-binding surface on Uba3 β-grasp domain undergoes a conformational transition.

E Sonay Elgin1, Nazlı Sökmen, Francis C Peterson

  • 1Department of Chemistry, Muğla Sıtkı Koçman University, Muğla 48000, Turkey. selgin@mu.edu.tr

Proteins
|July 24, 2012
PubMed
Summary

The E1-activating enzyme

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Functional Characterization of RING-Type E3 Ubiquitin Ligases In Vitro and In Planta
10:27

Functional Characterization of RING-Type E3 Ubiquitin Ligases In Vitro and In Planta

Published on: December 5, 2019

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Cellular Biology

Background:

  • Ubiquitin (Ub) and ubiquitin-like (Ubl) protein conjugation regulates cellular processes.
  • E1-activating enzymes are crucial for Ub/Ubl activation and transfer to E2-conjugating enzymes.
  • The NEDD8 E1 activating enzyme is a heterodimer of APPBP1 and Uba3 subunits.

Purpose of the Study:

  • To investigate the conformational dynamics of the Uba3-βGD domain in the NEDD8 E1 activating enzyme.
  • To determine the role of Uba3-βGD in E2-binding specificity.
  • To elucidate the mechanism of E1-E2 interaction.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy to study Uba3-βGD in solution.
  • Analysis of crystal structures of free E1 and NEDD8-E1 complex.
  • Comparison with SUMO E1 conformational transitions.

Main Results:

  • Uba3-βGD is an independently folded domain in solution.
  • Residues critical for E2 binding are absent from the NMR spectrum, indicating conformational flexibility.
  • The E2-binding surface of Uba3-βGD interconverts between multiple conformations.

Conclusions:

  • The E2-binding surface of Uba3-βGD exhibits conformational flexibility.
  • This flexibility allows for interconversion between multiple conformational substates.
  • Conformational flexibility is a key feature of E1-E2 interactions in ubiquitination pathways.