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Related Concept Videos

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...
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...
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,...
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...

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Evolution of allostery in the cyclic nucleotide binding module.

Natarajan Kannan1, Jian Wu, Ganesh S Anand

  • 1Department of Chemistry and Biochemistry, University of California, Gilman Drive, La Jolla, California 92093-0654, USA.

Genome Biology
|December 14, 2007
PubMed
Summary

Cyclic nucleotide binding (CNB) domains have evolved diverse signaling functions by adapting their structure to bind various molecules. This study reveals evolutionary mechanisms of allosteric regulation in CNB domains.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Biochemistry

Background:

  • Cyclic nucleotide binding (CNB) domains are crucial regulators of signaling pathways in diverse organisms.
  • Understanding CNB domain evolution and function is key to deciphering cellular responses to second messengers like cAMP.

Purpose of the Study:

  • To explore the evolutionary diversity of CNB domains and their signaling mechanisms.
  • To investigate how CNB domains elicit cellular responses upon ligand binding.

Main Methods:

  • Analysis of evolutionary information from genomic sequences, including the Global Ocean Sampling dataset.
  • Identification and classification of CNB domains and their associated functional domains.
  • Statistical comparison of functional constraints on canonical and non-canonical cyclic adenosine monophosphate (cAMP) binding domains.

Main Results:

  • CNB domains are frequently fused to various functional domains and exhibit significant evolutionary sequence variation.
  • The cyclic adenosine monophosphate (cAMP) binding pocket, specifically the phosphate-binding (PBC) motif, shows notable differences, influencing ligand specificity (e.g., heme binding in cooA family).
  • A key arginine in the PBC motif has co-evolved with a distal glycine, mediating allosteric coupling of ligand binding to regulatory sites.

Conclusions:

  • CNB domains function as versatile scaffolds for sensing diverse second messenger signals.
  • A proposed mechanism for allosteric regulation by CNB domains is supported by sequence, structural, and biochemical data.