Enzymes and Mechanisms within the UPS

**119**

**Chapter 7**

*Elena Santonico*

**Abstract**

KHNYN, N4BP1

**1. Introduction**

New Insights into the Mechanisms

Functional Specificities

Underlying NEDD8 Structural and

Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins are small polypeptides that are conjugated to substrates affecting their activity and stability. Cells encode "receptors" containing Ub-/Ubl-binding domains that interpret and translate each modification into appropriate cellular responses. Among the different Ubls, NEDD8, which is the ubiquitin's closest relative, retains many of the structural determinants that enable ubiquitin the ability to target proteins to degradation. Nevertheless, the direct involvement of NEDD8 conjugation to proteasome recruitment has been proved only in a few cases. To date, well-defined major NEDD8 substrates are primarily members of the cullin family, and cullin neddylation does not appear to mark these proteins for degradation. Various studies have demonstrated that selectivity between ubiquitin and NEDD8 is guaranteed by small but substantial differences. Nevertheless, several issues still need to be addressed, mainly concerning which interaction surfaces mediate NEDD8 function and what domains recognize them. Recently, two novel domains identified in KHNYN and N4BP1 proteins have shed new light on this research area. Here, I discuss some recent reports that contributed to shed light on the mechanisms underlining the discrimination between ubiquitin and NEDD8. Understanding the details of these molecular mechanisms represents a prominent facet for the identification of new therapeutic targets.

**Keywords:** NEDD8, ubiquitination, neddylation, ubiquitin-binding domains,

Protein diversity in living organisms is the result of several mechanisms acting at different steps of gene expression. Alternative splicing determines the production of a variety of proteins from a single pre-mRNA, and different promoters and termination sites increase the protein diversity during gene transcription. An additional level of complexity is achieved through posttranslational modifications (PTMs). More than 90,000 individual PTMs have been detected using biochemical and biophysical methods [1]. These modifications extend proteome diversity by inducing structural changes, such as the covalent binding of functional groups (phosphate, acetyl, methyl, lipids, and others) or the cleavage and the selective degradation of regulatory subunits. Such modifications in turn play a central role in regulating protein function, as they finely tune intermolecular interactions that modulate almost all biological processes. Thus, it is not surprising that almost 5% of the human genome

#### **Chapter 7**
