ABSTRACT
Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24)1,2. This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. 3). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER.
Subject(s)
Endoplasmic Reticulum , Protein Processing, Post-Translational , Ribosome Subunits, Large, Eukaryotic , Ubiquitin-Protein Ligases , Adaptor Proteins, Signal Transducing/metabolism , Binding Sites , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/ultrastructure , Cryoelectron Microscopy , Endoplasmic Reticulum/metabolism , Endoplasmic Reticulum/ultrastructure , Homeostasis , Intracellular Membranes/metabolism , Peptidyl Transferases/chemistry , Peptidyl Transferases/metabolism , Peptidyl Transferases/ultrastructure , Ribosomal Proteins/chemistry , Ribosomal Proteins/metabolism , Ribosomal Proteins/ultrastructure , RNA, Transfer/metabolism , SEC Translocation Channels/chemistry , SEC Translocation Channels/metabolism , SEC Translocation Channels/ultrastructure , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/ultrastructure , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/ultrastructure , Ribosome Subunits, Large, Eukaryotic/chemistry , Ribosome Subunits, Large, Eukaryotic/metabolism , Ribosome Subunits, Large, Eukaryotic/ultrastructureABSTRACT
Several pathologies have been associated with the AAA+ ATPase p97, an enzyme essential to protein homeostasis. Heterozygous polymorphisms in p97 have been shown to cause neurological disease, while elevated proteotoxic stress in tumours has made p97 an attractive cancer chemotherapy target. The cellular processes reliant on p97 are well described. High-resolution structural models of its catalytic D2 domain, however, have proved elusive, as has the mechanism by which p97 converts the energy from ATP hydrolysis into mechanical force to unfold protein substrates. Here, we describe the high-resolution structure of the p97 D2 ATPase domain. This crystal system constitutes a valuable tool for p97 inhibitor development and identifies a potentially druggable pocket in the D2 domain. In addition, its P61 symmetry suggests a mechanism for substrate unfolding by p97. DATABASE: The atomic coordinates and structure factors have been deposited in the PDB database under the accession numbers 6G2V, 6G2W, 6G2X, 6G2Y, 6G2Z and 6G30.