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J. Biol. Chem., Vol. 261, Issue 26, 11992-11999, 09, 1986
The protein substrate binding site of the ubiquitin-protein ligase system
A Hershko, H Heller, E Eytan and Y Reiss
In order to gain insight into the mechanisms that determine the selectivity
of the ubiquitin proteolytic pathway, the protein substrate binding site of
the ubiquitin-protein ligase system was identified and examined. Previous
studies had shown that the ligase system consists of three components: a
ubiquitin-activating enzyme (E1), ubiquitin-carrier protein (E2), and a
third enzyme, E3, the mode of action of which has not been defined. E3 from
rabbit reticulocytes was further purified by a combination of affinity
chromatography, hydrophobic chromatography, and gel filtration procedures.
A 180-kDa protein was identified as the subunit of E3. Two independent
methods indicate that E3 has the protein binding site of the ubiquitin
ligase system. These are the chemical cross-linking of 125I-labeled
proteins to the E3 subunit and the functional conversion of enzyme-bound
labeled proteins to ubiquitin conjugates in pulse-chase experiments. The
trapping of E3-bound protein for labeled product formation was allowed by
the slow dissociation of E3 X protein complex. The specificity of binding
of different proteins to E3, examined by both methods, showed a direct
correlation with their susceptibility to degradation by the ubiquitin
system. Proteins with free alpha-NH2 groups, which are good substrates,
bind better to E3 than corresponding proteins with blocked NH2 termini,
which are not substrates. Oxidation of methionine residues to sulfoxide
derivatives greatly increases the susceptibility of some proteins to
ligation with ubiquitin, with a corresponding increase in their binding to
E3. However, a protein derivative which was subjected to both amino group
modification and oxidation binds strongly to the enzyme, even though it
cannot be ligated to ubiquitin. It thus seems that the substrate binding
site of E3 participates in determining the specificity of proteins that
enter the ubiquitin pathway of protein degradation.

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