Protein Name

Trapped UBL activation complex



Biological Context

Post-translational modification with ubiquitin-like proteins (UBLs), such as ubiquitin, NEDD8 and SUMO, is an essential eukaryotic regulatory mechanism. One of the most important functions of UBLs is labeling proteins, which results in the proteasomal degradation. For that purpose, UBLs are required to be activated. Ubiquitin activation is caused by some conjugated reactions, in which E1, E2, and E3 enzymes involved. These reaction are composed of five steps as follows:

  1. E1 (APPBP1-UBA3) binds ATP, Mg2+ and the UBL (NEDD8), and catalyses adenylation of the C-terminal region in the UBL.
  2. The catalytic cysteine in E1 enzyme attacks the adenylated UBL, producing a thioester bond between the catalytic cysteine in E1 enzyme and the C-terminal region in the UBL.
  3. The E1 enzyme also binds another UBL at the adenylation site. Thus, the E1 enzyme has two UBLs during the activation cycle.
  4. The E1 enzyme having two UBLs associates with an E2 enzyme (Ubc12), and transthiolation reaction occurs, which results in transferring the UBL connected by thioester bonds with the E1, to the E2 enzyme.
  5. The UBL-E2 complex associates with an E3 enzyme, which facilitates UBL transfer to the target.

Thus, UBLs are activated and bind to the target via the dynamic E1-E2-E3 enzyme cascades (also see the entry: PDB:2QYU). In the reference article, the authors determined the structure of a trapped activation complex for the NEDD8 pathway, to understand the molecular switches influencing E1, E2 and UBL interactions.

Structure Description


Fig. 1 represents the whole structures reported in this article, which is separated by color in each domain. These structures contain seven modules: heterodimeric E1 (APPBP1-UBA3), two NEDD8s, a catalytically inactive E2 (Ubc12), and MgATP.

Fig. 1 The complex of APPBP1-UBA3-NEDD8s-MgATP-Ubc12

In the E1-E2-E3 enzyme cascades, UBL(T) is readily transferred from the E1 to E2 enzyme, which results in the difficulty to determine the structure of the activation complexes containing an E1, UBL(T), UBL(A) and an E2. To deal with this problem and trap an activation complex, the authors mutated a cystein to alanine residue in the E2 enzyme. This enabled them to have the E2 enzyme catalytically inactivated and to get the activation complex.

The E1 enzymes have the three common modules: an adenylation domain, a catalytic cysteine domain, and a domain structurally resembling ubiquitin (the ubiquitin-fold domain, UFD). In this article, APPBP1-UBA3 is reported as the E1 enzyme.

In the complex, the three domains in the APPBP1-UBA3 form a large central groove. A crossover loop connecting the adenylation and catalytic domains divides the groove into two clefts (Fig. 2). These clefts capture the MgATP, Ubc12, and two NEDD8s.

Fig. 2 The complex of APPBP1-UBA3-NEDD8s-MgATP-Ubc12

NEDD8(T) is in the center of the complex (Fig. 1). Electrostatic network exist between APPBP1-UBA3 and NEDD8(T) domains (Fig. 3). These networks contribute to APPBP1-UBA3-NEDD8(T) and Ubc12-NEDD8 complex formation. These electrostatic networks are considered to be the common mechanism in E1-UBL and E2-UBL complex formations.

Fig. 3 The electrostatic network of APPBP1-UBA3-NEDD8(T)

Protein Data Bank (PDB)



Huang, D.T. Hunt, H.W. Zhuang, M. Ohi, M.D. Holton, J.M. Schulman, B.A.; "Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity."; Nature; (2007) 445:394-398 PubMed:17220875.


  • PDB:2QYU E3 like protein (explanation of ubiquitin related protein degradation system is included)

author: Daisuke Kuroda

Japanese version:PDB:2NVU