Editing Anaphase-promoting complex (section)

== Substrate recognition ==
APC/C substrates have recognition amino acid sequences that enable the APC/C to identify them.  The most common sequence is known as the destruction box or D-box. APC/C brings together an E2 [[ubiquitin-conjugating enzyme]] and the D-box rather than being an intermediate covalent carrier.<ref>{{cite journal | vauthors = King RW, Deshaies RJ, Peters JM, Kirschner MW | s2cid = 25369228 | title = How proteolysis drives the cell cycle | journal = Science | volume = 274 | issue = 5293 | pages = 1652–9 | date = December 1996 | pmid = 8939846 | doi = 10.1126/science.274.5293.1652 | bibcode = 1996Sci...274.1652K }}</ref>  The D-box should have a version of the following [[amino acid]] sequence: RXXLXXXXN, where R is [[arginine]], X is any amino acid, L is [[Leucine]], and N is [[asparagine]].  The Ken-box is another motif of importance.  Its sequence should resemble the one that follows: KENXXXN, where K is [[lysine]] and E is [[glutamate]].  The last amino acid position in the Ken-box is highly variable. Though it has been shown that mutations in the sequences do inhibit destruction of the proteins "in vivo", there is still much to learn about how proteins are targeted by the APC/C.<ref name= "Morgan_2007" />

Once bound to APC/C, Cdc20 and Cdh1 serve as D and KEN box receptors for various APC substrates. Kraft ''et al.'' have shown that the substrates' D boxes bind directly to the highly conserved [[WD40 repeat]] propeller region on the APC activators. It is important to note that the conserved area of the propeller of Cdh1 is much larger than that of Cdc20, allowing Cdh1 to have a broader substrate specificity, consistent with the fact that APC/C<sup>Cdh1</sup> also activates APC-mediated destruction of KEN box containing substrates. The D box further enhances protein degradation, for Lysine residues in close proximity to the D box serve as targets of ubiquitylation. It has been found that a Lys residue immediately C-terminal to the D box can function as a ubiquitin acceptor.<ref>{{cite journal | vauthors = Kraft C, Vodermaier HC, Maurer-Stroh S, Eisenhaber F, Peters JM | title = The WD40 propeller domain of Cdh1 functions as a destruction box receptor for APC/C substrates | journal = Molecular Cell | volume = 18 | issue = 5 | pages = 543–53 | date = May 2005 | pmid = 15916961 | doi = 10.1016/j.molcel.2005.04.023 | doi-access = free }}</ref>

Many APC substrates contain both D and KEN boxes, with their ubiquitylation by either APC/C<sup>Cdc20</sup> or APC/C<sup>Cdh1</sup> dependent on both sequences, yet some substrates contain only either a D box or a KEN box, in one or multiple copies. Having two distinct degradation sequences creates a high level of substrate specificity on the APC/C, with APC/C<sup>Cdc20</sup> being more dependent on the D box and APC/C<sup>Cdh1</sup> more dependent on the KEN box. For example, APC/C<sup>Cdh1</sup> is capable of ubiquitylating KEN box-only-containing substrates like Tome-1 and Sororin.<ref name = "Barford" />

Although Cdc20 and Cdh1 may serve as D and KEN box receptors, the low affinity of these co-activator–substrate interactions suggests that it is unlikely that the co-activators alone are sufficient to confer high-affinity substrate binding to the APC/C<sup>Cdc20</sup> and APC/C<sup>Cdh1</sup>.<ref name = "Barford" /> Consequently, core APC/C subunits, like Apc10, contribute towards substrate association as well. In APC/C constructs lacking the Apc10/Doc1 subunit, substrates like Clb2 are unable to associate with APC<sup>Δdoc1</sup>–Cdh1, while addition of purified Doc1 to the APC<sup>Δdoc1</sup>–Cdh1 construct restores the substrate binding ability.<ref name = "Passmore" />