RCSB PDB - 2MWS: Structure of the complex of ubiquitin and the ubiquitin-like (UBL) domain of Ddi1 (original) (raw)
DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin.
[Nowicka, U.](/search?q=citation.rcsb%5Fauthors:Nowicka, U.), [Zhang, D.](/search?q=citation.rcsb%5Fauthors:Zhang, D.), [Walker, O.](/search?q=citation.rcsb%5Fauthors:Walker, O.), [Krutauz, D.](/search?q=citation.rcsb%5Fauthors:Krutauz, D.), [Castaneda, C.A.](/search?q=citation.rcsb%5Fauthors:Castaneda, C.A.), [Chaturvedi, A.](/search?q=citation.rcsb%5Fauthors:Chaturvedi, A.), [Chen, T.Y.](/search?q=citation.rcsb%5Fauthors:Chen, T.Y.), [Reis, N.](/search?q=citation.rcsb%5Fauthors:Reis, N.), [Glickman, M.H.](/search?q=citation.rcsb%5Fauthors:Glickman, M.H.), [Fushman, D.](/search?q=citation.rcsb%5Fauthors:Fushman, D.)
(2015) Structure 23: 542-557
PubMed Abstract:
Ddi1 belongs to a family of shuttle proteins targeting polyubiquitinated substrates for proteasomal degradation. Unlike the other proteasomal shuttles, Rad23 and Dsk2, Ddi1 remains an enigma: its function is not fully understood and structural properties are poorly characterized. We determined the structure and binding properties of the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains of Ddi1 from Saccharomyces cerevisiae. We found that while Ddi1UBA forms a characteristic UBA:ubiquitin complex, Ddi1UBL has entirely uncharacteristic binding preferences. Despite having a ubiquitin-like fold, Ddi1UBL does not interact with typical UBL receptors but unexpectedly binds ubiquitin, forming a unique interface mediated by hydrophobic contacts and by salt bridges between oppositely charged residues of Ddi1UBL and ubiquitin. In stark contrast to ubiquitin and other UBLs, the β-sheet surface of Ddi1UBL is negatively charged and therefore is recognized in a completely different way. The dual functionality of Ddi1UBL, capable of binding both ubiquitin and proteasome, suggests an intriguing mechanism for Ddi1 as a proteasomal shuttle.
Organizational Affiliation:
Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.