Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p (original) (raw)

Many ubiquitinated proteins are recognized by do-200 First Street SW mains that specifically bind to mono-and/or polyubiqui-Rochester, Minnesota 55905 tin. These include the UEV, UBA, UIM, and CUE domains or motifs (reviewed in Buchberger, 2002). The UEV domain is a counterpart of a ubiquitin-conjugating enzyme, Summary as illustrated by the structure of the enzymatically inactive TSG101 UEV domain (Pornillos et al., 2002). The Coupling of ubiquitin conjugation to ER degradation other three prominent ubiquitin binding domains, UBA, (CUE) domains are ‫05ف‬ amino acid monoubiquitin UIM, and CUE, are all small (20-50 amino acids) and are binding motifs found in proteins of trafficking and ubiknown or predicted to be ␣-helical. The ubiquitin binding quitination pathways. The 2.3 Å structure of the Vps9p-UBA domain is found in DNA damage-inducible and CUE domain is a dimeric domain-swapped variant of other proteins (Hofmann and Bucher, 1996). UBA dothe ubiquitin binding UBA domain. The 1.7 Å structure mains are three-helix bundles (Dieckmann et al., 1998; of the CUE:ubiquitin complex shows that one CUE Withers-Ward et al., 2000; Mueller and Feigon, 2002) dimer binds one ubiquitin molecule. The bound CUE that can bind polyubiquitin with high affinity, and their dimer is kinked relative to the unbound CUE dimer physiological functioning is in at least some cases mediand wraps around ubiquitin. The CUE monomer conated by polyubiquitin binding (Wilkinson et al., 2001; tains two ubiquitin binding surfaces on opposite faces Funakoshi et al., 2002). UBA domains also bind monoof the molecule that cannot bind simultaneously to ubiquitin (Vadlamudi et al., 1996; Bertolaet et al., 2001b; a single ubiquitin molecule. Dimerization of the CUE Chen et al., 2001), bind to other proteins (Dieckmann et domain allows both surfaces to contact a single ubial., 1998; Withers-Ward et al., 2000), and form homoquitin molecule, providing a mechanism for high-affinand heterodimers with each other (Bertolaet et al., ity binding to monoubiquitin. 2001a). The UIM (ubiquitin interaction motif; Hofmann and Falquet, 2001) is a ubiquitin binding motif discov-Introduction ered in the proteasome subunit S5a. The S5a UIM binds polyubiquitin, but not monoubiquitin (Deveraux et al., The covalent addition of ubiquitin and ubiquitin-like pro-1994). In contrast, UIMs of many endocytic proteins bind teins is one of the most widespread regulatory postmonoubiquitinated proteins. The endocytic proteins eptranslational modifications of proteins (Hershko and Ciesin, eps15, Vps27p/Hrs, and Hse1p contain UIMs that chanover, 1998; Hochstrasser, 2000; Pickart, 2001). bind monoubiquitin (Bilodeau et al., 2002; Klapisz et al., Ubiquitin is a 76 amino acid protein named for its ex-2002; Oldham et al., 2002; Polo et al., 2002; Raiborg et traordinary distribution from yeast to man. The C termial., 2002; Shih et al., 2002; Shekhtman and Cowburn, nus of ubiquitin is conjugated to Lys residues of target 2002). The UIMs of eps15 are essential for the ubiquitinaproteins by the action of three enzymes: an ubiquitintion of eps15 itself, representing a second function for activating enzyme (E1), an ubiquitin-conjugating en-UIMs in promoting the ubiquitination of proteins that zyme (E2), and an ubiquitin protein ligase (E3). contain them (Polo et al., 2002). Ubiquitin is conjugated to proteins via an isopeptide The most recent addition to the family of ubiquitin bond between the C terminus of ubiquitin and a specific binding domains is the coupling of ubiquitin conjugation Lys residue in the ubiquitinated protein. Ubiquitin may to ER degradation (CUE) domain, which is found in roughly 50 different proteins (Ponting, 2000, 2002; Batebe attached to proteins as a monomer or as a polyubiquiman et al., 2002). CUE domains are named for the yeast tin chain. Ubiquitin polymers are formed when additional Cue1p protein, which recruits the ubiquitin-conjugating ubiquitin molecules are attached to Lys residues on a enzyme Ubc7p to the ER, where it is essential for misfolded protein degradation (Biederer et al., 1997). Other *Correspondence: james.hurley@nih.gov CUE domain proteins include the autocrine motility fac-3 These authors contributed equally to this work. tor receptor (AMFR), a ubiquitin protein ligase also in-4 Present address: Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland 20892. volved in protein degradation at the ER (Fang et al., Deveraux, Q., Ustrell, V., Pickart, C., and Rechsteiner, M. (1994). A 26 S protease subunit that binds ubiquitin conjugates. J. Biol. Chem. 269, 7059-7061. We thank B. Beach for DNA sequencing, A. Hickman for critical comments on the manuscript, G. Miller and R. Trievel for assistance Dieckmann, T., Withers-Ward, E.S., Jarosinksi, M.A., Liu, C.-F., with data collection, and A. Weissman for discussions. This study Chen, I.S.Y., and Feigon, J. (1998). Structure of a human DNA repair was supported in part by NIH grant number GM55301 to B.F.H. and protein UBA domain that interacts with HIV-1 Vpr. Nat. Struct. Biol. a predoctoral fellowship from the HHMI to B.A.D. We acknowledge 5, 1042-1047. use of the SBC-CAT and SER-CAT beamlines at the APS, ANL.