PROSITE documentation PDOC50033

UBX domain profile

Covalent modification of proteins by the small, evolutionary conserved protein ubiquitin (see <PDOC00271>) plays a central role in a variety of cellular processes, including bulk protein degradation, cell-cycle control, stress response, DNA repair, signal transduction, transcriptional regulation and vesicular traffic. A cascade of three enzymes (called E1, E2 and E3) catalyzes the conjugation of ubiquitin to lysine side-chains of target proteins. Ubiquitination is a reversible process: several specific ubiquitin carboxy-terminal hydrolases (UBPs) (see <PDOC00750>) can remove ubiquitin from proteins. The variety of cellular processes regulated by ubiquitination demands a high substrate specificity of the ubiquitination machinery as well as the existence of diverse downstream effector proteins interacting with ubiquitinated substrates. Most of these cellular effectors are characterized by a modular composition of ubiquitin-binding motifs and further domains mediating specific functions. The UBX domain is an about 80 amino acid residue module of unknown function present typically at the carboxyl terminus of a variety of eukaryotic proteins. It was originally identified in the human hypothetical 33.4 kDa protein, a member of the UBA domain (see <PDOC50030>) family of proteins implicated in ubiquitination processes. The UBX domain is found also in a number of different proteins that so far appear unrelated to processes involving ubiquitination, including FAS-associated factor-1 (FAF1), p47 and Rep8, as well as in several proteins of unknown function. As only very few UBX domain proteins have been studied in details, no general function for the UBX domain has yet emerged [1,2].

The resolution of the three dimensional of the UBX domain of human FAF1 shows a β-Grasp fold characterized by a β-β-α-β-β-α-β secondary-structure organization (see <PDB:1H8C>). The strands are arranged into a mixed five-stranded β sheet in the order 21534. The three dimensional structure of the UBX domain reveals a close structural relationship with ubiquitin despite the lack of significant sequence homology [1].

Some proteins known to contain an UBX domain are listed below:

• Mammalian FAS-associated factor 1 (FAF1). It specifically interacts with the cytoplasmic domain of FAS.
• Mammalian P97/VCP associated protein p47, involved in homotypic ER and Golgi fusion control.
• Mammalian UBX domain-containing protein 1 (UBXD1).
• Human hypothetical 33.4 kDa protein (Y33K).
• Human reproduction 8 protein (rep-8).
• Human undulin 2, a matrix glycoprotein.
• Yeast SHP1 protein.
• Yeast hypothetical proteins YBR273C, YDL091C, YDR330W, YJL048C, YMR067C.

The profile we developed covers the entire UBX domain.