@article {18695,
	title = {Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {16},
	year = {2009},
	month = {2009///},
	pages = {883 - 889},
	abstract = {Ubiquitin (denoted Ub) receptor proteins as a group must contain a diverse set of binding specificities to distinguish the many forms of polyubiquitin (polyUb) signals. Previous studies suggested that the large class of ubiquitin-associated (UBA) domains contains members with intrinsic specificity for Lys63-linked polyUb or Lys48-linked polyUb, thus explaining how UBA-containing proteins can mediate diverse signaling events. Here we show that previously observed Lys63-polyUb selectivity in UBA domains is the result of an artifact in which the dimeric fusion partner, glutathione S-transferase (GST), positions two UBAs for higher affinity, avid interactions with Lys63-polyUb, but not with Lys48-polyUb. Freed from GST, these UBAs are either nonselective or prefer Lys48-polyUb. Accordingly, NMR experiments reveal no Lys63-polyUb{\textendash}specific binding epitopes for these UBAs. We reexamine previous conclusions based on GST-UBAs and present an alternative model for how UBAs achieve a diverse range of linkage specificities.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb.1637},
	url = {http://www.nature.com/nsmb/journal/v16/n8/abs/nsmb.1637.html},
	author = {Sims,Joshua J. and Haririnia,Aydin and Dickinson,Bryan C. and Fushman, David and Cohen,Robert E.}
}
@article {18699,
	title = {Diverse polyubiquitin interaction properties of ubiquitin-associated domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {12},
	year = {2005},
	month = {2005///},
	pages = {708 - 714},
	abstract = {The ubiquitin-associated (UBA) domain occurs frequently in proteins involved in ubiquitin-dependent signaling pathways. Although polyubiquitin chain binding is considered to be a defining feature of the UBA domain family, the generality of this property has not been established. Here we have surveyed the polyubiquitin interaction properties of 30 UBA domains, including 16 of 17 occurrences in budding yeast. The UBA domains sort into four classes that include linkage-selective polyubiquitin binders and domains that bind different chains (and monoubiquitin) in a nondiscriminatory manner; one notable class (30\%) did not bind any ubiquitin ligand surveyed. The properties of a given UBA domain are conserved from yeast to mammals. Their functional relevance is further suggested by the ability of an ectopic UBA domain to alter the specificity of a deubiquitylating enzyme in a predictable manner. Conversely, non-UBA sequences can modulate the interaction properties of a UBA domain.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb962},
	url = {http://www.nature.com/nsmb/journal/v12/n8/full/nsmb962.html},
	author = {Raasi,Shahri and Varadan,Ranjani and Fushman, David and Pickart,Cecile M.}
}
