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Related Concept Videos

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...
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,...
The ADP/ATP Carrier Protein01:42

The ADP/ATP Carrier Protein

ADP/ATP carrier or AAC protein is the most abundant carrier protein in the inner mitochondrial membrane. It transports large quantities of ADP and ATP, equivalent to the average human body weight, every day. Among other transporters, ACC protein is one of the best-studied members of the mitochondrial carrier protein family. The ADP/ATP carrier protein comprises two transmembrane helices connected to a loop and a single alpha-helix on the matrix side. It switches between two conformational...
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...
Amino acids03:42

Amino acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...

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Related Experiment Video

Updated: May 30, 2026

Chemical Modification of the Tryptophan Residue in a Recombinant Ca2+-ATPase N-domain for Studying Tryptophan-ANS FRET
12:07

Chemical Modification of the Tryptophan Residue in a Recombinant Ca2+-ATPase N-domain for Studying Tryptophan-ANS FRET

Published on: October 9, 2021

Structure and function of the AAA+ nucleotide binding pocket.

Petra Wendler1, Susanne Ciniawsky, Malte Kock

  • 1Gene Center, Ludwig-Maximilians-Universität München, München, Germany. wendler@genzentrum.lmu.de

Biochimica Et Biophysica Acta
|August 16, 2011
PubMed
Summary
This summary is machine-generated.

AAA+ proteins are vital molecular machines. Subtle differences in their nucleotide-binding pockets, particularly arginine finger and sensor 2 residues, explain functional diversity among AAA+ ATPase subgroups.

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Last Updated: May 30, 2026

Chemical Modification of the Tryptophan Residue in a Recombinant Ca2+-ATPase N-domain for Studying Tryptophan-ANS FRET
12:07

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Published on: October 9, 2021

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • AAA+ proteins are a superfamily of molecular machines.
  • They are essential for numerous cellular processes.
  • Understanding their nucleotide-binding pocket is key to their function.

Purpose of the Study:

  • To review structural and functional data of the AAA+ protein nucleotide-binding pocket.
  • To compare conserved motifs and their roles in AAA+ protein function.
  • To assess how variations in these motifs contribute to functional diversification.

Main Methods:

  • Overlaying Protein Data Bank (PDB) structures of related AAA+ ATPases.
  • Displaying biologically relevant motifs within the nucleotide-binding pocket.
  • Illustrating inter-protomer interactions based on oligomeric structures.

Main Results:

  • Conserved motifs in the nucleotide-binding pocket are crucial for ATP binding, hydrolysis, oligomerization, and communication.
  • Subtle differences in arginine finger and sensor 2 residues were observed between AAA+ subgroups.
  • These variations suggest a mechanism for functional diversification within the AAA+ superfamily.

Conclusions:

  • The nucleotide-binding pocket of AAA+ proteins exhibits conserved features and subgroup-specific variations.
  • Variations in key residues like the arginine finger and sensor 2 contribute to the diverse functions of AAA+ proteins.
  • This comparative analysis provides insights into the structure-function relationships of this essential protein superfamily.