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Related Concept Videos

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...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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 pathway,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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UBXD1 binds p97 through two independent binding sites.

Maximilian Kern1, Vanesa Fernandez-Sáiz, Zasie Schäfer

  • 1Max Planck Institute of Biochemistry, Department of Molecular Cell Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.

Biochemical and Biophysical Research Communications
|January 29, 2009
PubMed
Summary

The p97 protein

Area of Science:

  • Cellular Biology
  • Protein Biochemistry

Background:

  • The p97 protein (also known as VCP) is a crucial chaperone involved in the ubiquitin-proteasome system.
  • Numerous cofactors regulate p97's diverse cellular functions, often binding via UBX or PUB domains.

Purpose of the Study:

  • To investigate the molecular mechanisms of UBXD1 cofactor interaction with the p97 protein.
  • To determine the roles of UBXD1's UBX and PUB domains in p97 binding.

Main Methods:

  • Biochemical assays to assess protein-protein interactions.
  • Cellular experiments to validate binding in living cells.

Main Results:

  • The PUB domain of UBXD1 mediates strong binding to the C-terminus of p97.
  • The UBX domain of UBXD1 does not significantly contribute to p97 binding.

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  • A novel binding site on UBXD1 competes with the p47 cofactor for interaction with the N-domain of p97.

    • Conclusions:

    • UBXD1 utilizes a bipartite binding mode to interact with p97.
    • This unique interaction suggests UBXD1 is a potent regulator of p97 cofactor dynamics.