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Related Concept Videos

ATP Synthase: Mechanism01:48

ATP Synthase: Mechanism

In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear genome encodes the majority of ATP synthase subunits, the mitochondrial genome encodes some of the enzyme's most critical components. The formation of this multi-subunit enzyme is a complex multi-step process regulated at the level of transcription, translation, and assembly. Defects in one or more of these steps can result in decreased ATP...
ATP Synthase: Structure01:18

ATP Synthase: Structure

ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in response to the electrochemical gradient, producing ATP from ADP and inorganic phosphate. ATP synthase can also work in a reverse direction by hydrolyzing ATP and generating an electrochemical gradient. Different forms of ATP synthases have evolved special features to meet the specific demands of the cell. Based on their specific feature, ATP...
ATP Driven Pumps III: V-type Pumps01:30

ATP Driven Pumps III: V-type Pumps

V-type pumps are ATP-driven pumps found in the vacuolar membranes of plants, yeast, endosomal and lysosomal membranes of animal cells, plasma membranes of a few specialized eukaryotic cells, and some prokaryotes. They are also known as the V1Vo-ATPase, that couple ATP hydrolysis to transport protons against a concentration gradient.
The peripheral or cytosolic V1 domain with eight subunits is involved in ATP hydrolysis. The integral or transmembrane V0 domain containing at least five subunits...
ATP Driven Pumps I: An Overview01:27

ATP Driven Pumps I: An Overview

ATP-driven pumps, also known as transport ATPases, are integral membrane proteins. They have binding sites for ATP located on the membrane's cytosolic side and the ion-conducting domain in the transmembrane region. These pumps use the free energy released from ATP hydrolysis to move the solutes across cell membranes against an electrochemical gradient.
There are four main types of ATP-driven pumps - P-type, V-type, F-type, and ABC transporter. All these pumps are of varying complexities and are...
ATP Driven Pumps II: P-type Pumps01:34

ATP Driven Pumps II: P-type Pumps

The P-type pumps are a large family of integral membrane transporter ATPases. They are divided into five major types based on substrate specificity, from I to V.
A typical P-type pump has three cytosolic domains: nucleotide-binding (N), phosphorylation (P), and activator (A) domains. These domains are connected to the membrane-spanning helices by short amino acid segments. ATP hydrolysis and covalent phosphoenzyme intermediate formation are crucial parts of the catalytic cycle. At the highly...
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,...

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Visualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB.

Sukyeong Lee1, Jae-Mun Choi, Francis T F Tsai

  • 1Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

Molecular Cell
|January 25, 2007
PubMed
Summary

ClpB molecular chaperones disaggregate damaged proteins. ATP binding drives ClpB conformational changes, enabling high-affinity substrate capture and threading for protein repair.

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Area of Science:

  • Protein folding and molecular chaperones
  • Biochemistry and structural biology
  • Cellular stress response mechanisms

Background:

  • ClpB is a crucial molecular chaperone responsible for disaggregating misfolded or damaged proteins.
  • Understanding ClpB's mechanism is vital for comprehending cellular protein quality control.
  • Previous studies have implicated ATP hydrolysis in ClpB's function, but structural details remain elusive.

Purpose of the Study:

  • To elucidate the structural mechanisms underlying ATP-dependent protein disaggregation by ClpB.
  • To investigate the role of nucleotide binding states in ClpB conformational dynamics.
  • To provide a structural basis for ClpB's high-affinity substrate binding and translocation.

Main Methods:

  • Electron cryomicroscopy (cryo-EM) to determine high-resolution structures of ClpB.
  • Biochemical assays to assess substrate binding and nucleotide dependence.
  • Analysis of ClpB structures in various nucleotide-bound states (ATP-activated, AMPPNP, ADP, nucleotide-free).

Main Results:

  • Cryo-EM reconstructions reveal distinct ClpB conformations across different nucleotide states.
  • Motif 2 of the ClpB M domain plays a key role in mediating ATP-driven conformational changes in the AAA-1 ring.
  • ATP is essential for high-affinity substrate binding, with AMPPNP being insufficient.
  • Stabilization of D1 loops in the central pore in the ATP-activated state underpins high-affinity substrate binding.

Conclusions:

  • ClpB utilizes ATP hydrolysis to drive conformational changes for protein disaggregation.
  • A mechanism is proposed where ClpB captures substrates via its upper AAA-1 ring surface.
  • Substrate threading through the ClpB hexamer is an ATP hydrolysis-dependent process.