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Related Concept Videos

ATP Driven Pumps II: P-type Pumps01:34

ATP Driven Pumps II: P-type Pumps

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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...
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ATP Driven Pumps III: V-type Pumps01:30

ATP Driven Pumps III: V-type Pumps

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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...
5.2K
ATP Driven Pumps I: An Overview01:27

ATP Driven Pumps I: An Overview

10.4K
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...
10.4K
ATP Synthase: Structure01:18

ATP Synthase: Structure

17.4K
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...
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Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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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...
6.9K
ATP Synthase: Mechanism01:48

ATP Synthase: Mechanism

18.8K
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...
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Related Experiment Video

Updated: Mar 28, 2026

Measuring In Vitro ATPase Activity for Enzymatic Characterization
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Measuring In Vitro ATPase Activity for Enzymatic Characterization

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Computational Classification of P-Type ATPases.

Dan Søndergaard1,2, Michael Knudsen1, Christian Nørgaard Storm Pedersen3,4

  • 1Bioinformatics Research Centre (BiRC), Aarhus University, C. F. Møllers Allé 8, DK-8000, Aarhus C, Denmark.

Methods in Molecular Biology (Clifton, N.J.)
|December 24, 2015
PubMed
Summary
This summary is machine-generated.

Computational methods and databases can identify P-type ATPase protein sequences. This analysis is crucial for modern molecular biology and protein classification, determining subtypes efficiently.

Keywords:
ClassificationDatabasesMotif detectionP-type ATPase sProtein sequences

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Measuring Cation Transport by Na,K- and H,K-ATPase in Xenopus Oocytes by Atomic Absorption Spectrophotometry: An Alternative to Radioisotope Assays
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Measuring Cation Transport by Na,K- and H,K-ATPase in Xenopus Oocytes by Atomic Absorption Spectrophotometry: An Alternative to Radioisotope Assays

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A Semi-High-Throughput Adaptation of the NADH-Coupled ATPase Assay for Screening Small Molecule Inhibitors
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Measuring Cation Transport by Na,K- and H,K-ATPase in Xenopus Oocytes by Atomic Absorption Spectrophotometry: An Alternative to Radioisotope Assays
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A Semi-High-Throughput Adaptation of the NADH-Coupled ATPase Assay for Screening Small Molecule Inhibitors
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Sequence data analysis is fundamental in modern molecular biology.
  • Computational methods offer efficient ways to infer protein information.
  • Identifying protein families and functions is essential for biological research.

Purpose of the Study:

  • To provide a guide on using computational methods for protein sequence analysis.
  • To demonstrate how to classify protein sequences as P-type ATPases.
  • To enable the identification of specific P-type ATPase subtypes.

Main Methods:

  • Utilizing freely available biological databases.
  • Employing computational methods for sequence classification.
  • Implementing motif detection algorithms for functional inference.

Main Results:

  • Successfully classified protein sequences based on P-type ATPase characteristics.
  • Distinguished between different subtypes of P-type ATPases.
  • Validated the efficacy of computational approaches for sequence annotation.

Conclusions:

  • Freely available databases and computational tools are powerful resources for P-type ATPase identification.
  • The described methods facilitate accurate protein classification and subtype determination.
  • This approach enhances the efficiency of analyzing large-scale sequence data in molecular biology.