3D Structure of Ubiquitin

CPK Color Scheme
 C O N P S
Ubiquitin is a small (8.5kD) protein present in all eukaryotic cells. Its 76 amino acid sequence is so highly conserved that nearly identical versions exist in a variety of organisms; yeast and human ubiquitin, for example, differ at only 3 of the 76 residues. It is involved in multiple cellular functions: protein degredation, chromatin structure, and heat shock.

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Click here to see a cartoon image of ubiquitin's structure, colored to indicate alpha-helix (maroon), beta-sheet (yellow), turns (blue), and unstructured (white) regions.

Ubiquitin is a remarkably stable protein, more than usually resistant to extremes of pH and temperature. Its compact structure and abundant hydrogen bonds contribute to its stability.
Click here to view ubiquitin's hydrogen bonding (bonds are orange).

Also contributing to ubiquitin's stability and compactness is its hydrophobic core.
Click here to highlight ubiquitin's hydrophobic residues.

Ubiquitin covalently modifies proteins by forming isopeptide bonds between its own C-terminal carboxyl group and the target protein's side-chain lysine residue amino group to form a branched polypeptide. The terminal amino acid, glycine 76, appears to be crucial in the binding process; ubiquitin is inactivated when proteolytic cleavage removes this terminal glycine.
Click here to highlight the C-terminus; glycine 76 is shown in CPK colors.

A ubiquitin molecule can bind to other ubiquitin molecules, forming multi-ubiquitin chains. This process is a pre-requisite for the targeting of most proteins for degredation. Lysine 48 is a probable site of isopeptide bond formation for the next ubiquitin molecule.
Click here to highlight lysine 48.

Ubiquitin's sequence includes multiple lysine residues; it is possible that another of these lysines participates in the binding process as well.
Click here to highlight all the lysines in ubiquitin. (Rotate this image to see all seven lysines clearly.)

References

Bernd, K. 2002 October. Class Lecture.

Nottingham University Biochemistry Dept. The Ubiquitin System. http://www.nottingham.ac.uk/biochemcourses/students/ub/ubindex.html Accessed 2003 April 8.

Liao, Yu-Pei. Ubiquitin. http://life.nthu.edu.tw/~b821720/hk/ubi/ubi.htm Accessed 2003 April 9.