APPBP1-UBA3-NEDD8: An E1-ubiquitin-like protein complex with ATP (PDB ID: 1R4N)
Created by Kathleen Sink
Ubiquitin-activating enzymes, or E1 enzymes, are important in catalyzing the first part of the ubiquitination reaction (2). This process marks a protein for degradation. In turn, the process of degradation regulates the function of proteins in many organisms. Ubiquitin activating enzymes are key components of the ubiquitin proteasome system. This E1 enzyme contributes to proteolytic cleavage of tagged proteins and ubiquitylation of proteins (1). The protein APPBP1-UBA3-NEDD8 is an E1-ubiquitin-like protein complex with ATP and plays a significant role in the cell cycle. The molecular weight of APPBP1-UBA3-NEDD8 is 8728.86 g/mol. The isoelectric point occurs at pH 5.51 (5).
APPBP1-UBA3-NEDD8 protein is found in Homo sapiens and was studied using Escherichia coli. Since it is an E1 enzyme, it affects processes such as cell division and embryo development. This is because ubiquitin and their associated proteins regulate many of these processes. APPBP1-UBA3-NEDD8 is important to this system because if it were absent, then the necessary proteins would not be degraded in cells. The lack of important proteins can lead to problems with cell homeostasis and ultimately lead to disease (1).
The structure of proteins affects their function and ability to perform their roles in biological reactions. Structure is especially imnportant in this case because the structure specificity ultimately coordinates the ubl with the correct pathway in the ubiquitination reaction (2). The A-128. The side chain of UBA3 is positioned in a way to coordinate a Mg 2+ ion (2).
Both the APPBP1-UBA3 and NEDD8 parts can undergo conformational changes so they can drive teh activation reaction (2). Two forms include the free and complexed APPBP1-UBA3 and NEDD8 forms. The E1 conformational change is important because it causes a domain to move, make space for NEDD8 and secure the NEDD8 C terminus in the active site. How this is secured exactly is unknown, other than the change in shape when the domain moves and accomodates the NEDD8. The different conformations drive downstream reactions in the transfer cascade (2).
The biological function of APPBP1-UBA3-NEDD8 can be compared to other proteins of similar primary and tertiary structure. According to the protein BLAST results, one protein with similar primary structure to APPBP1-UBA3-NEDD8 is a trapped ubiquitin-like protein (UBL) activation-like complex (6) (PDB ID: 2NVU). It is part of the Mgatp-Ubc12 complex. The trapped UBL activation-like complex contains NEDD8 subunits. It shares similar ligands to APPBP1-UBA3-NEDD8 including ATP, zinc, and the magnesium ion. The protein produced by this search showed a low E value (3e-40), which indicates sequence similarity to APPBP1-UBA3-NEDD8. According to the Dali server results, the low RMSD value of 0.7 shows that there are three-dimensional structural similarities. The Z score of 50.8 exemplifies the similarity between the two tertiary structures (4).
The protein in comparison to APPBP1-UBA3-NEDD8 serves as a thioester switch toggling E1-E2 affinity. It is all part of an E1-E2-E3 cascade complex. According to Huang, E1 enzymes activate UBLs by catalysing UBL carboxy-terminal adenylation, forming a covalent E1-UBL thioester intermediate, and generating a thioester-linked E2 UBL product, which must be released for subsequent reactions (7). In relation to this E1-E2-E3 complex, there are two E2 binding sites that depend on NEDD8 being thioester-linked to E1. E2 enzymes are important in the second step of ubiquitination. One is uncovered by an E1 conformational change. The second comes right from the thioester-bound NEDD8. Once the NEDD8 is transfered to E2, going back to another E1 conformation would help with the release of the E2-NEDD8 thioester product. Therefore, transferring the UBL's thioester linkage between conjugation enzymes can cause conformational changes and affect interaction networks to drive consecutive steps in UBL cascades (7).
As shown above, E1 protein is important to many biological functions. Like many other enzymes, it greatly helps in biological reactions, regulates our cells, and helps in maintaining cell homeostasis. The importance of structure and how it influences a protein's function can also be seen from the images shown.