title: DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin.
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.
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
authors.forename: Urszula
authors.initials: U
authors.lastname: Nowicka
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
authors.forename: Daoning
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Institut des Sciences Analytiques, UMR5280-Université de Lyon, 69100 Villeurbanne, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Walker
authors.affiliation: Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa, Israel.
authors.forename: Daria
authors.initials: D
authors.lastname: Krutauz
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Castañeda
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
authors.forename: Apurva
authors.initials: A
authors.lastname: Chaturvedi
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
authors.forename: Tony Y
authors.initials: TY
authors.lastname: Chen
authors.affiliation: Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa, Israel.
authors.forename: Noa
authors.initials: N
authors.lastname: Reis
authors.affiliation: Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa, Israel.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Glickman
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA. Electronic address: fushman@umd.edu.
authors.forename: David
authors.initials: D
authors.lastname: Fushman
mesh_terms: D006860:Hydrogen Bonding; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry*
chemical_list: C108125:DDI1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D025801:Ubiquitin