Structure and recognition of polyubiquitin chains of different lengths and linkage

Abstract

The polyubiquitin signal is post-translationally attached to a large number of proteins, often directing formation of macromolecular complexes resulting in the translocation, assembly or degradation of the attached protein. Recent structural and functional studies reveal general mechanisms by which different architectures and length of the signal are distinguished.

Figure 1.. Architecture of polyubiquitin chains

Unanchored chains are shown here. These are often found attached to a target protein via an isopeptide bond between the free C-terminus of the proximal ubiquitin and an amino group on the target protein. Chains can be “linear” (no more than one amino group of each ubiquitin is linked to another ubiquitin) or “branched” (at least one ubiquitin is attached to other ubiquitins via two or more different amino groups). The ubiquitin containing the free C-terminus is the “proximal” subunit and the ubiquitin(s) lacking any amino group linkage is a “distal subunit”. The polymers are referred to as “homogeneous” if all linkages use the same amino group on each ubiquitin. They are termed “heterogeneous” if ubiquitin linkages involve different amino groups on different subunits. Chains containing other ubiquitin-like proteins are called “heterologous” or “mixed”. The type of linkage is designated by the identity of the amino group used, i.e. Met1-, Lys6-, Lys11-, Lys27-, Lys29-, Lys33-, Lys48-, Lys63-linked. Note that Met1-linked ubiquitin is identical to the proprotein product of the polyubiquitin gene and has often been referred to as linear polyubiquitin. We propose the Met1-linked nomenclature to avoid the confusion with unbranched chains described above. In the “open” conformations the hydrophobic patch of ubiquitin is exposed, while in the “closed” conformations this patch is buried by ubiquitin-ubiquitin interactions. Abbreviations: SUMO, small ubiquitin-like modifier.

Figure 2.. Specific recognition of polyubiquitin chains by deubiquitinating enzymes

Modes of recognition by deubiquitinating enzymes involve: a) binding to the proximal ubiquitin and the ubiquitinated protein resulting in removal (amputation) of the chain; b) binding to the distal copy of ubiquitin only resulting in shortening (distal trimming) of the chain; c) binding to the specific linkage and/or faces of ubiquitin uniquely juxtaposed by that linkage resulting in specific cleavage of one type of linkage; or d) binding of adjacent ubiquitins in a chain by a deubiquitinating enzyme containing multiple ubiquitin binding domains, each bound to a single ubiquitin (pan specific). Abbreviations: Ub, ubiquitin. Reprinted with permission from Reyes-Turcu FE, Wilkinson KD. Polyubiquitin binding and disassembly by deubiquitinating enzymes. Chem Rev. 2009 Apr;109(4):1495-508. Copyright 2009, American Chemical Society.

Figure 3.. Figure 3. Length dependence of linear chain structure and recognition

Each row represents a different length of linear ubiquitin: a) extended chains with exposed hydrophobicity such as Met1- and Lys63-linked; b) closed conformations where some of the ubiquitins contain intramolecularly buried hydrophobic patches as seen in Lys48-linked chains [67, 88, 89]; c) length selection by binding to a single receptor polypeptide (UBA [ubiquitin associated domain]2 of hHR23a and USP5 [ubiquitin-specific protease 5] are shown [18, 39]); and d) combinatorial length selection by two different ubiquitin receptors (RPN10 and DSK2 are shown [56]). Abbreviations: UBA, ubiquitin-associated domain; UBL, ubiquitin-like; UBX, ubiquitin regulatory X domain; USP, ubiquitin-specific protease; ZnF, zinc finger.