Ubiquitin folding

Figure 5.9. Split ubiquitin as a sensor for protein-protein interactions. Protein A is fused to the N-terminal domain and protein B is fused to the C-terminal domain of ubiquitin. Interaction of A and B reconstitutes a full-sized, folded ubiqutin. The folded ubiquitin is recognized by a specific protease and cleavage releases the reporter protein.

Chromatin is composed of nucleosomes, where each comprise 147 base pairs of DNA wrapped around an octamer oftwo copies of each histone H2A, H2B, H3, and H4. Nucleosomes are folded into higher-order structures that are stabilized by linker histones. Chromatin structure can be altered by enzymes that posttranslationally modify histones (e.g., through phosphorylation, acetylation, methylation, or ubiquitination) or by ATP-driven chromatin-remodeling complexes that alter nucleosome position and/or composition. 

Proteosomal degration is the process by which improperly folded proteins or proteins with altered post-translational modifications are removed from a cell before they have a detrimental effect on cellular function. This is performed in small organelles known as proteosomes. Proteins are targeted for destruction in the proteosome by having a number of small ubiquitin molecules added. 

Small tfbiquitin-like modifier represents a family of evolutionary conserved proteins that are distantly related in amino-acid sequence to ubiquitin, but share the same structural folding with ubiquitin proteins. SUMO proteins are covalently conjugated to protein substrates by an isopeptide bond through their carboxyl termini. SUMO addition to lysine residues of target proteins, termed SUMOylation, mediates post-transla-tional modification and requires a set of enzymes that are distinct from those that act on ubiquitin. SUMOylation regulates the activity of a variety of tar get proteins including transcription factors. 

Expressing recombinant proteins as N-terminal fusions with ubiquitin [109] is another strategy that can help to achieve proper folding. Additionally, this is an elegant way to obtain proteins that do not start with a methionine residue, since the ubiquitin moiety is cleaved off by endogenous ubiquitin-specific proteases [100]. 

The Crystal Structure of MoaD Reveals the Ubiquitin Fold 23... 

Increasing evidence suggests that evolution has used (and is using) the E2 fold for new purposes. In one apparent example of functional expansion, E2 core domains have been observed to be embedded within much larger polypeptide chains [140, 141]. The functional properties of these massive E2s remain poorly characterized, and it is likely that more of them will be discovered. But the clearest case of functional diversification is provided by the UEV proteins. UEVs are related to E2s in their primary, secondary, and tertiary structures, but they lack an active-site cysteine residue and therefore cannot function as canonical E2s [142]. Nonetheless they play several different roles in ubiquitin-dependent pathways. 

Cyr, D. M., Hohfeld, J. and Patterson, C. Protein quality control U-box-containing E3 ubiquitin ligases join the fold. Trends Biochem Sd 2002, 27, 368-75. 

While the functional analogy between ThiS, MoaD, and ubiquitin-like modifiers is widely accepted, the two protein classes are frequently described as unrelated sometimes even a convergent evolution to the energetically favorable ubiquitin fold is discussed. Despite these claims, there is a statistically significant sequence... 

The three-dimensional structure of both UBA domains of the human Rad23a proteins have been solved and reveal a conserved three-helix bundle fold [50, 51], So far, no structure of a UBA-ubiquitin complex is known and we can only speculate on their mode of interaction. The original UBA structures revealed two... 

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