Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

14.1K
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...
14.1K
Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
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...
5.0K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

6.5K
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...
6.5K
Protein Complex Assembly02:41

Protein Complex Assembly

16.6K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
16.6K
Nucleoid01:24

Nucleoid

849
The nucleoid represents a structurally and functionally distinct region within prokaryotic cells, where the cell's DNA and associated proteins are housed. Unlike eukaryotic cells, prokaryotes lack a membrane-bound nucleus, and the nucleoid facilitates the organization and accessibility of the genetic material within this constraint. The DNA in most bacteria and archaea exists as a single, circular, double-stranded molecule that is highly compacted through supercoiling and interactions with...
849
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.5K
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...
5.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Characterization of the Flavor Profiles of Fresh and Hot-Air-Dried Ginger (<i>Zingiber officinale</i> Roscoe) by Molecular Sensory Science.

Foods (Basel, Switzerland)·2026
Same author

Relationship between cerebrospinal fluid neurobiomarkers and symptoms in older patients with cognitive impairment: an observational clinical study.

Scientific reports·2026
Same author

Effects of Compound Probiotics on Production Performance, Apparent Digestion Rate of Nutrients and Serum Index of Pigs at Different Stages.

Animals : an open access journal from MDPI·2026
Same author

Structural composition and functional diversities of G proteins in fungi.

Mycology·2026
Same author

Efficient inverse design of long-wave infrared metalenses: frequency-domain physics-model-informed neural networks.

Optics express·2026
Same author

Active carbon-fixing microbes and their role in carbon fixation in mangrove sediments.

Marine pollution bulletin·2026

Related Experiment Video

Updated: Jan 18, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.2K

Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing.

Chunyan Meng1, Xiaoyan Shi2, Wenting Guo3

  • 1China-New Zealand Joint Laboratory on Biomedicine and Health, Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China.

Structure (London, England : 1993)
|September 12, 2025
PubMed
Summary

The E. coli enzyme YqfB, containing an ASCH domain, metabolizes N4-acetylcytidine (ac4C) nucleosides. Structural and in vivo studies reveal its specific function in ac4C metabolism and substrate preferences in related proteins.

Keywords:
ASCH domainCrystal structureRNA modificationac(4)Camidohydrolase

More Related Videos

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

3.7K
Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

10.3K

Related Experiment Videos

Last Updated: Jan 18, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.2K
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

3.7K
Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

10.3K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • ASC-1 homology (ASCH) domain proteins are implicated in RNA metabolism, yet their structures and functions remain poorly understood.
  • The E. coli enzyme YqfB, possessing an ASCH domain, exhibits amidohydrolase activity, converting N4-acetylcytidine (ac4C) RNA nucleosides to cytidine.

Purpose of the Study:

  • To elucidate the structural basis of EcYqfB's amidohydrolase activity and its interaction with N4-acetylcytidine.
  • To investigate the in vivo function of EcYqfB in ac4C metabolism.
  • To explore the structural and functional diversity within the ASCH domain protein family through homologous proteins.

Main Methods:

  • X-ray crystallography was employed to determine the structures of EcYqfB in unbound and substrate-bound states.
  • In vivo experiments involving gene deletion were conducted to assess the physiological role of EcYqfB.
  • Structural determination of homologous proteins, mouse EOLA1 and human TRIP4-ASCH domain, was performed.

Main Results:

  • Crystal structures revealed the detailed interaction between EcYqfB and its substrate, providing insights into the catalytic mechanism.
  • In vivo studies demonstrated that EcYqfB deletion does not affect global ac4C levels, indicating a specific role in nucleoside metabolism rather than RNA modification.
  • Structural analysis of EOLA1 and TRIP4-ASCH domain highlighted variations in substrate preferences among ASCH domain proteins.

Conclusions:

  • EcYqfB specifically functions in the metabolism of ac4C nucleosides, not in the direct modification of RNA.
  • The study provides crucial structural insights into the ASCH domain family, paving the way for future functional characterization.
  • Comparative structural analysis reveals potential differences in substrate specificity within the ASCH domain protein family.