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Vol. 10, Issue 3, 741-756, March 1999
Department of Biochemistry and Molecular Biology, University of
Chicago, Chicago, Illinois 60637
The Saccharomyces cerevisiae Doa4
deubiquitinating enzyme is required for the rapid degradation of
protein substrates of the ubiquitin-proteasome pathway. Previous work
suggested that Doa4 functions late in the pathway, possibly by
deubiquitinating (poly)-ubiquitin-substrate intermediates associated
with the 26S proteasome. We now provide evidence for physical and
functional interaction between Doa4 and the proteasome. Genetic
interaction is indicated by the mutual enhancement of defects
associated with a deletion of DOA4 or a proteasome
mutation when the two mutations are combined. Physical association of
Doa4 and the proteasome was investigated with a new yeast 26S
proteasome purification procedure, by which we find that a sizeable
fraction of Doa4 copurifies with the protease. Another yeast
deubiquitinating enzyme, Ubp5, which is related in sequence to Doa4 but
cannot substitute for it even when overproduced, does not associate
with the proteasome. DOA4-UBP5 chimeras were made by a
novel PCR/yeast recombination method and used to identify an N-terminal
310-residue domain of Doa4 that, when appended to the catalytic domain
of Ubp5, conferred Doa4 function, consistent with Ubp enzymes having a
modular architecture. Unlike Ubp5, a functional Doa4-Ubp5 chimera
associates with the proteasome, suggesting that proteasome binding is
important for Doa4 function. Together, these data support a model in
which Doa4 promotes proteolysis through removal of ubiquitin from
proteolytic intermediates on the proteasome before or after initiation
of substrate breakdown.
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