In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest and most versatile family. However, few PUX proteins have been structurally or functionally characterized and how they participate in the substrate processing of CDC48A is not fully understood. Here, we first performed a comparative bioinformatic analysis, in which we found that the PUX proteins can be functionally divided into six types. We used this classification as a guide for our experimental efforts to elucidate how PUX proteins mediate client recognition and delivery for CDC48A-mediated unfolding. As a first step in this experimental analysis, we cloned and expressed a number of PUX protein constructs, we assessed their interaction features, and obtained crystals for several PUX domains. These bioinformatic and experimental results provide a basis for the in-depth structural and functional analysis of how PUX proteins control the CDC48A segregase.