Many cellular and secreted proteins are chemically modified after their translation is completed. The covalent linkage of a polypeptide chain (modifier) to a substrate protein is a special case of post-translational modification. In the late seventies it was observed that ubiquitin, a small modifier, marks short-lived proteins for degradation by the 26S proteasome. Over the last decade many other ubiquitin-related proteins were discovered and isolated. Attachment of polypeptide chains onto acceptor molecules became a common feature to regulate spatially and timely organized cellular pathways of proteins. This article focuses on the structures of the three modifiers: ubiquitin, RUB and SUMO and the cognate enzymes involved in these modification pathways. We have described the homologies and differences of these proteins and indicate salient topological hallmarks common to modifier-conjugating enzymes. This characterization will help in understanding these regulatory pathways and their similarities and differences in controlling protein fate, from protein degradation signals generated by polyubiquitination to functional modification brought about by RUB and SUMO conjugation.