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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding and Linkage

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...

Conserved Binding Sites

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...

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Related Experiment Video

Updated: Mar 31, 2026

Author Spotlight: Characterizing Novel Enzymes from Extremophiles and Common Pathogens to Understand DNA Repair and Replication

Author Spotlight: Characterizing Novel Enzymes from Extremophiles and Common Pathogens to Understand DNA Repair and Replication

Published on: July 5, 2024

From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase.

Maiko Tanabe¹, Yoshizumi Ishino², Hirokazu Nishida¹

¹Central Research Laboratory, Hitachi Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan.

Archaea (Vancouver, B.C.)

|October 29, 2015

Summary

DNA ligases are crucial enzymes for genetic engineering and DNA sequencing. This review details their in vitro applications, ligation mechanisms, and engineered variants based on structural insights.

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Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

DNA ligases are essential enzymes found in all living cells, playing a vital role in DNA repair and replication.
They are widely applied in molecular biology techniques, including genetic engineering and DNA sequencing.
Despite their importance, protein engineering efforts for DNA ligases have lagged behind those for DNA polymerases.

Purpose of the Study:

To review the diverse applications of DNA ligases in in vitro gene manipulation techniques.
To summarize recent advancements in understanding DNA ligation mechanisms through structural biology.
To present examples of engineered DNA ligases developed using insights from their three-dimensional structures.

Main Methods:

Literature review of DNA ligase applications in molecular biology.
Analysis of published tertiary structures of DNA ligases to elucidate reaction mechanisms.
Compilation of examples of engineered DNA ligases and their design principles.

Main Results:

DNA ligases have a broad range of applications in in vitro gene manipulation.
Recent structural studies have significantly advanced the understanding of DNA ligation mechanisms.
Engineered DNA ligases with improved properties have been developed based on structural information.

Conclusions:

DNA ligases are versatile tools in molecular biology, with ongoing structural and engineering advancements.
Further research into DNA ligase structure-function relationships can lead to novel biotechnological applications.
The review highlights the potential for protein engineering to enhance DNA ligase utility.