Structural and Functional Studies of Ubiquitin Binding Domains

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There are now at least sixteen known ubiquitin binding domains domains. The structures of many of the complexes with monoubiquitin have been determined, revealing interactions with multiple surfaces on ubiquitin. Inroads into understanding polyubiquitin specificity have been made for two UBA domains, whose structures have been characterized in complex with Lys48-linked diubiquitin. Several ubiquitin binding domains, including the UIM, CUE, and A20 ZnF, promote autoubiquitination, which regulates the activity of proteins that contain them. At least one of these domains, the A20 ZnF, acts as a ubiquitin ligase by recruiting a ubiquitin:ubiquitin conjugating enzyme thiolester adduct in a process that depends on the ubiquitin-binding activity of the A20 ZnF. The affinities of the monoubiquitin binding interactions of these domains span a wide range, but are most commonly weak, with Kd > 100 microM. The weak interactions between individual domains and monoubiquitin are leveraged into physiologically relevant high affinity interactions via several mechanisms: ubiquitin polymerization, modification multiplicity, oligomerization of ubiquitinated proteins and binding domain proteins, tandem binding domains, binding domains with multiple ubiquitin binding sites, and cooperativity between ubiquitin binding and binding through other domains to phospholipids and small G-proteins. The yeast Vps27Hse1 complex and homologous mammalian HrsSTAM complex deliver ubiquitinated transmembrane proteins to the ESCRT endosomal sorting pathway. Vps27 is a multimodular protein containing VHS, FYVE, UIM domains, a core region, and an unstructured motif-rich C-terminus. Hse1 contains VHS, UIM, and SH3 domains, a core region, and an unstructured region. These proteins are paradigms for proteins that contain multiple low-affinity ubiquitin binding domains. The structures and interactions of these domains have been characterized in isolation. The Vps27 FYVE domain, which was previously crystallized in our laboratory, is responsible for binding with moderate affinity to the endosomal lipid phosphatidylinositol 3-phosphate. The individual UIM domains bind ubiquitin with very low affinity. The Vps27Hse1 complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. We have solved the crystal structure of the core responsible for the assembly of the Vps27Hse1 complex at 3.0 Angstrom resolution. The structure consists of two intertwined GAT domains, each consisting of two helices from one subunit and one from the other. The two GAT domains are connected by an antiparallel coiled-coil to form a 90 -long barbell-like structure. In collaboration with Juan Bonifacino (NICHD) we found that the integrity of the core structure was required for efficient physiological trafficking function. This structure places the domains of Vps27 and Hse1 that recruit ubiquitinated cargo and deubiquitinating enzymes close to each other. Coarse-grained Monte Carlo simulations of the Vps27Hse1 complex on a membrane (collaboration with Gerhard Hummer, NIDDK) show how the complex binds cooperatively to lipids and ubiquitinated membrane proteins and acts as a scaffold for ubiquitination reactions. The cooperative binding to membranes and up to three ubiquitinated cargo proteins offers a mechanism for functional recognition, despite the low affinity of the individual UIM:ubiquitin interactions.