ubiquitin

A highly conserved protein involved in tagging proteins for degradation by the cell, part of the waste-disposal machinery.

Proteins in the cell are always in a state of flux. New ones are being created as old ones are destroyed. This keeps partially unfolded or degraded proteins from hanging around and mucking up the works. Also, protein disposal systems allow molecules that are only important for a short period of time, such as signalling proteins, to be rapidly flushed out of the system as they are no longer wanted. Proteins like ubiqutin can label the trash and help guide it to the lysosome, where it will be digested.

Ubiquitin is a 76 amino acid (about 8.5 kDa) protein found in most eukaryotes. It is highly conserved (yeast and human proteins are 53% identical!). Ubiquitin ligates to proteins, committing them to the degradation pathway. There are three accessory enzymes that are involved in tagging a protein with ubiquitin, creatively named E₁, E₂ and E₃. The following schematic shows the chain of events involved in ubiquitination of a protein:

	E1 - the ubiquitin activating enzyme

		             E1
(1)	Ubiquitin-C-O + ATP ----> P-P + Ubiquitin-C~AMP
	          "			          "
                  O			          O
	(carbonyl from the C-term	   (ubiquitinyl acyladenylate)
	    glycine)

(2)	Ubiquitin-C~AMP + E1-SH ----> AMP + Ubiquitin-C~S-E1 
		  "           	    	              "
		  O                                   O            
					     (thioester)

	E2 - ubiquitin carrier protein

(3)	E2-SH + Ubiqutin-C~S-E1 ----> E1-SH + Ubiquitin-C~S-E2
			 "				"
                         O                              O

	E3 - ligase

	E3 + target protein ----> E3:target protein

	E3:target + E2-S~C-Ubiquitin ----> E2-SH + E3 + Protein-Ubiquitin
			 "
			 O

Proteins are targeted on free amino groups such as the N-terminus or the sidechain amino group on lysine. Ubiquitin itself has exposed surface lysines which can be tagged, sometimes leading to chains of ubiquitin attached to a target protein.