Ubc9

Ubc9 is a ubiquitin conjugating enzyme (E2) whose function involves transfer of ubiquitin or small ubiquitin-like modifier (SUMO) from ubiquitin activating enzyme (E1) to its designated substrate. is specifically involved in SUMO transfer^[1].

Structure

Murine/human Ubc9 exhibits a single domain structure consisting of both alpha helices and beta-pleated sheets (PDB: 1U9A). has been identified as the active residue and is located on a loop of amino acids (78-108) between beta sheet four and alpha helix two ^[1]. Amino acids surrounding the active site have been shown to play a role in catalysis of SUMO transfer to substrate via the suppression the the substrate lysine side chain pKa, which serves the purpose of nucleophile activation^[2].

Crystal structure has shown that Ubc9 is the central protein in the SUMO-RanGAP1-Ubc9-Nup358 (PDB: 1Z5S), which forms in such a way as to enhance conjugation and transfer of the SUMO to substrate ^[3].

Along with the formation of a thioester bond the its substrate, Ubc9 can also interact noncovelently with SUMO. Crystal structure of the (PDB: 2UYZ) shows that the Ubc9 residues involved in this interaction are located at the end of helix one, on beta strand one, and along the following loop. These residues were shown to interact with the beta sheet of SUMO1 ^[4].

Function

Ubc9 is enzymatically involved in the SUMOylation process. It is the enzyme responsible for ligating the SUMO to the protein. Depending on whether the reaction is done in vitro, it will ligate the SUMO directly to the substrate, and if done in vivo, the SUMO will be ligated to the conjugating enzyme and then put onto the substrate^[5]. Initially, a thioester bond is formed between the SUMO and the E1 enzyme via an ATP-dependent reaction. The SUMO is then transferred to the active cystein of the E2, in this case, Ubc9. The SUMO is then ligated to a lysine side chain amino group of the substrate, during which an E3 enzyme may or may not be recruited. The use of E3 mediated transfer serves functions such as increasing the specificity for the substrate to be SUMOylated ^[4].

Kinetic analysis has shown that the Ubc9 amino acids , which are in close proximity to the active site Cys93, play a role in substrate recongnition within the thioester Ubc9-SUMO1 complex. These amino acids are not found in other E2 enzymes, making their involvement in SUMO conjugation unique to Ubc9^[6].

SUMOylation has been shown to enhance processes such as DNA methyltransferse 1 enzymatic activity, which has a major regulatory effect on gene transcription ^[7]. The transcription factor AP-2 is SUMOylated by Ubc9, a process which decreases the transcription activation potential of AP-2, thus having an effect on gene transcription, and therefore likely having an effect on gene expression as well^[8].

Noncovalent interaction between Ubc9 and SUMO distant from the active site have been shown to be critical in the formation of SUMO chains, upon which in vivo functions such as metabolic regulation and signaling are dependent. Mutagenesis studies on the noncovalent Ubc9-SUMO1 complex have shown that Ubc9H20D and SUMO1E67R mutation cause inhibition of noncovalent interaction between the two, and thus inhibit complex formation. A similar interaction is seen in the Ubc9-SUMO2 complex ^[4]. Lack of noncovalent interaction between Ubc9 and SUMO2 has been shown to inhibit SUMO2 chain formation ^[4]. NMR studies of Ubc9 have shown that noncovalent interaction between SUMO-1 and Ubc9 play a critical role in the transfer of SUMO-1 from the activating enzyme (E1) to the conjugating enzyme (E2)^[9].

Disease

Expression of Ubc9 has been found to be related to causing human diseases such as cancer, neurodegenerative diseases, and heart diseases. Studies have shown it to interact with tumor suppressor proteins such as p53, p63, and p73 and fundamental in the tumor progression and preventing apoptotic pathways^[10].

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