TY - JOUR
T1 - DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin
AU - Nowicka, Urszula
AU - Zhang, Daoning
AU - Walker, Olivier
AU - Krutauz, Daria
AU - Castañeda, Carlos A.
AU - Chaturvedi, Apurva
AU - Chen, Tony Y.
AU - Reis, Noa
AU - Glickman, Michael H.
AU - Fushman, David
N1 - Funding Information:
We thank Emma Dixon for providing some di-Ub chains, Yaniv Kazansky and Christina Camara for Ub mutants, Hongpeng Wang for help with making Ddi1UBA, Dina Raveh for the original Ufo1 plasmid, Susan Krueger for help with SANS measurements, and Dina Schneidman-Duhovny for advice with SANS data analysis. This research was funded by NIH grant GM095755 to D.F. and M.H.G. and in part by a joint grant from the US-Israel Binational Foundation (BSF) to D.F. and M.H.G., and utilized NMR instrumentation supported in part by NSF grant DBI1040158. We acknowledge the support of NIST, US Department of Commerce, in providing the neutron research facilities used in this work.
Publisher Copyright:
©2015 Elsevier Ltd. All rights reserved.
PY - 2015/3/3
Y1 - 2015/3/3
N2 - 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.
AB - 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.
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U2 - 10.1016/j.str.2015.01.010
DO - 10.1016/j.str.2015.01.010
M3 - Article
C2 - 25703377
AN - SCOPUS:84923923110
SN - 0969-2126
VL - 23
SP - 542
EP - 557
JO - Structure
JF - Structure
IS - 3
ER -