Related Experiment Video
Updated: Apr 30, 2026
11:27
X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
Published on: May 13, 2020
3.4K
The dimerization domain in DapE enzymes is required for catalysis
Boguslaw Nocek1, Anna Starus2, Magdalena Makowska-Grzyska1
1Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
Plos One
|May 9, 2014
Summary
The dimerization domain is essential for the activity of DapE, an enzyme crucial for bacterial cell wall synthesis. Removing this domain inactivates the enzyme, highlighting it as a potential target for new antibiotics.
Area of Science:
- Biochemistry
- Structural Biology
- Microbiology
Background:
- Antibiotic resistance necessitates novel antimicrobial drug targets.
- Lysine and meso-diaminopimelic acid synthesis via the dap operon are vital for bacteria.
- Dap enzymes are potential targets for new antimicrobial agents.
Purpose of the Study:
- To investigate the role of the dimerization domain in DapE enzyme activity.
- To characterize dimerization domain deletion mutants of DapE from Haemophilus influenzae and Vibrio cholerae.
Main Methods:
- Engineering and characterization of dimerization domain deletion mutants.
- Structural analysis (X-ray crystallography).
- Biochemical assays and molecular dynamics simulations.
Main Results:
- Dimerization domain deletion mutants of DapE showed no enzymatic activity.
- Structural comparisons suggest the dimerization domain is critical for DapE function.
- Absence of the dimerization domain increased active site loop flexibility.
Conclusions:
- The dimerization domain is essential for DapE enzymatic activity.
- DapE's dimerization domain is a potential target for antimicrobial drug development.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
11.8K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.8K
00:59Mechanisms of Membrane Domain Formation
3.2K
Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
Another mechanism for membrane domain formation involves membrane proteins interacting with...
Another mechanism for membrane domain formation involves membrane proteins interacting with...
3.2K
01:30Assembly of Signaling Complexes
4.7K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
4.7K
01:07Catalytically Perfect Enzymes
4.3K
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Most enzymes...
Most enzymes...
4.3K
01:18Membrane Domains
6.2K
The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the...
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the...
6.2K
01:49Conserved Binding Sites
4.1K
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...
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...
4.1K