Related Experiment Video
Updated: Jun 22, 2026
07:05
Measuring Enzymatic Activity of Neurodevelopmental Disorder-Associated Deubiquitylating Enzymes via an In Vitro Ubiquitin Chain Cleavage Assay
Published on: September 27, 2024
The current structural and functional understanding of APOBEC deaminases
Ronda Bransteitter1, Courtney Prochnow, Xiaojiang S Chen
1Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Cellular and Molecular Life Sciences : CMLS
|June 24, 2009
Summary
The apolipoprotein B mRNA-editing enzyme catalytic polypeptide (APOBEC) family
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- The apolipoprotein B mRNA-editing enzyme catalytic polypeptide (APOBEC) family comprises cytidine deaminases with critical biological roles.
- These enzymes are implicated in diverse processes including lipid metabolism, immune system function, and host defense against viruses and mobile genetic elements.
- APOBEC proteins exert their functions by deaminating single-stranded DNA or RNA.
Purpose of the Study:
- To review recent structural and functional studies of the APOBEC deaminase family, with a focus on Apo3G.
- To facilitate understanding of APOBEC protein-nucleic acid interactions, substrate recognition, and oligomerization through structural analysis.
- To compare APOBEC structures with other zinc-coordinating deaminases.
Main Methods:
- High-resolution crystal structures of APOBEC proteins (Apo2, Apo3G-CD2).
- Nuclear Magnetic Resonance (NMR) structure determination of Apo3G-CD2.
- Comparative structural analysis of APOBEC family members and related deaminases.
Main Results:
- Availability of high-resolution crystal structures for key APOBEC family members.
- Detailed structural insights into Apo3G-CD2 obtained through both X-ray crystallography and NMR.
- Foundation laid for comparative analysis to elucidate functional mechanisms.
Conclusions:
- Structural data provides a basis for understanding APOBECs' roles in biological pathways.
- Further structural comparisons will illuminate substrate binding and oligomerization.
- Continued research on APOBEC structures is crucial for deciphering their diverse functions.
Related Concept Videos
01:13The Proteasome
Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin...
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin...
02:18The Proteasome
Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
02:23RNA Editing
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
01:17The Proteasome Structure
The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
The proteasome is an...
The proteasome is an...
02:34Enzymes
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
01:19Allosteric 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,...
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,...