The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
APCC activator-binding ABBA motif
Functional site description:
The complex E3 ligase APC/C is primarily active toward Anaphase in targeting proteins for proteosomal destruction. A hydrophobic groove located within the carboxyl-terminal WD40 repeat domain of APC/C activators, Cdc20/Cdh1 acts as a binding site for the ABBA motif. The motif was originally identified in A-type cyclins, Bub1, BubR1 and Acm1 - hence the name, ABBA motif, though it has also been called the Phe and A motif. The cyclin ABBA motif, found in Cyclin A and its yeast functional homologue Clb5, act as degrons and help to order the degradation of the key mitotic substrates of the APC/C. But, in addition to its role as a degradation signal, in Acm1 and BubR1, the ABBA motifs act as a pseudo substrate inhibitory motif. Its pseudosubstrate inhibitory property is exemplified in MCC-APC/C-Cdc20 complex which is crucial for the proper regulation of spindle assembly checkpoint. Furthermore, in BubR1 and Bub1, ABBA acts as a localization signal to recruit Cdc20 to the kinetochore.
ELMs with same func. site: LIG_APCC_ABBA_1  LIG_APCC_ABBAyCdc20_2 
ELM Description:
Amphipathic linear motif containing seven amino acids that appear at a relatively constant distance away from the D box motif. It was named the ‘ABBA motif’ since it was originally found in A-type cyclins (P78396), Bub1 (O43683), BubR1 (O60566), and Acm1 (Q08981). The divergent ABBA motif in B-type cyclin Clb5 in yeast facilitates Cdc20 binding and promotes degradation of Clb5 during mitosis by the APC/C (Lu,2014). The ABBA motif in yeast Clb5 which binds to yeast Cdc20 is distinct from the ABBA motif in yeast Acm1 which binds to Cdh1. Therefore the Clb5 class of motif requires a separate motif description from other ABBA motifs.
The yeast Cdc20 binding motif is present at residues 99-105 in Clb5. In contrast to the original ABBA motif, this motif starts with two highly conserved basic residues forming electrostatic interactions with a cluster of acidic residues (Asp311, Asp312, and Asp313) of yeast Cdc20. Another polar residue at position 3 follows and might augment Cdc20 binding. Positions 4 and 5 provide residues for hydrophobic interactions with the binding groove. The sixth position is highly flexible and thus may be dispensable for Cdc20 binding. Position 7 contains a negatively charged aspartate residue to stabilise the binding by electrostatic interactions (Lu,2014). Lack of an acidic cluster in other APC/C activators, such as its human CDC20 orthologue and yeast Cdh1 could be the reason why Clb5 fails to bind these proteins (Lu,2014). A similar motif is identified in yeast Mad3 and needs experimental evidence to ascertain its role in the yeast mitotic cycle.
Pattern: [KR]..[ILVM][FHY].[DE]
Pattern Probability: 0.0001669
Present in taxon: Fungi
Interaction Domain:
WD40 (PF00400) WD domain, G-beta repeat (Stochiometry: 1 : 1)
o See 2 Instances for LIG_APCC_ABBAyCdc20_2
o Abstract
In eukaryotes, each stage of the cell cycle is specifically controlled by the timely phosphorylation and degradation of mitotic proteins. Cyclin-dependent protein kinases (Cdks) and an ubiquitin protein ligase called the anaphase-promoting complex (APC/C or cyclosome) are central to this process. The APC/C activity oscillates during the cell cycle and promotes the degradation of its substrates in ordered groups. The APC/C activator proteins Cdc20 and Cdh1 act as the primary substrate interacting subunits and bind the substrate proteins through different degron motifs like the D box, KEN BOX, ABBA motif and some other non-canonical degrons (Davey,2016).
Cdc20 joins the APC/C in early mitosis and is then replaced by Cdh1 during anaphase. APC/C regulates mitosis by degrading cyclins, the regulatory subunits of cyclin-dependent kinases (CDKs), which control the cell cycle by phosphorylation of specific cell cycle related proteins. In addition, the APC/C controls the degradation of securin and other proteins, thereby triggering chromosome segregation in anaphase (Di Fiore,2015). During the mitotic phase of the cell cycle, chromosomes are separated into two identical sets. After duplication in S phase, a large protein complex assembles at each centromere, called the kinetochore. Kinetochores serve as docking site for attachment of chromatids to spindle microtubules during anaphase, thereby generating tension across sister chromatids. To prevent deficient chromatid separation, the spindle assembly checkpoint (SAC) is responsible for surveillance of the cell cycle. In early mitosis, activation of SAC leads to the formation of a mitotic checkpoint complex which contains proteins Mad2 and BubR1-Bub3 and also incorporates Cdc20 (Pines,2011). These proteins contain multiple sequence motifs that block the APC/C-Cdc20 from interacting with its bona fide substrates, acting as a pseudosubstrate inhibitor, and places the APC/C in a structural conformation that is inactive (Di Fiore et al., 2016, in press). This inhibition is mainly achieved by the cooperative activity of different degron motifs; among them the ABBA motifs found in the BubR1 protein plays a critical role. The inhibitory region of human BubR1 has four characterized motifs: an N-terminal KEN box and an evolutionarily conserved ABBA-KEN-ABBA cassette. The ABBA motifs at positions 272and 340 are required to stabilize the MCC onto the APC/C by binding the two CDC20 molecules in the MCC. The ABBA272 motif binds to Cdc20 associated with APC/C and ABBA340 binds to Cdc20 in the core MCC. And this ABBA motif mediated interaction in the SAC is essential for the ability of the MCC to rapidly inactivate the APC/C should a kinetochore-microtubule attachment be perturbed. A third ABBA motif in BubR1, also conserved in its paralogue Bub1, recruits Cdc20 to the kinetochore. Thus in BubR1 and BUB1, the ABBA motifs are necessary for the SAC to work at full strength and to recruit Cdc20 to kinetochores (Vleugel,2015; Di Fiore,2015). In metazoan cyclin A, the ABBA motif is required for its proper degradation via Cdc20 through competitive interaction with central SAC component BubR1 when the SAC is active in prometaphase (Di Fiore,2015), thereby setting up the ordered degradation of the key mitotic substrates of the APC/C substrates: Cyclin A, Cyclin B and Securin.
The ABBA motif, co-operating with a KEN box and D box, in yeast Acm1 acts as a pseudo substrate inhibitor for yeast Cdh1. Mutation of the KEN box and D box changes Acm1 to an efficient APC/C substrate and leads to its destruction through the ABBA motif (Enquist-Newman,2008). The functional homologue of cyclin A in yeast, Clb5, also contains an ABBA motif and is necessary for the correct ordering of protein destruction during mitotic exit in yeast (Lu,2014). Thus the ABBA motif is central to the recognition mechanism of APC/C-activator complex and is essential for the fidelity of cell cycle progression.
The ABBA binding site is less conserved than the KEN box or D box binding sites on the WD40 beta-propeller. The human Cdc20 ABBA binding pocket shares identical specificity determinants with the yeast Cdh1. However, the key interacting residues are highly diverged in human Cdh1. No known ABBA motif binds human Cdh1, and it is likely that it has lost its ability to interact with the motif. The specificity of the yeast Cdc20 ABBA motif binding pocket has diverged and favours a more basic residue at the N-terminus of the peptide.
Only a small number of ABBA motif based interactions have so far been investigated, limiting the full characterization of binding preference as well as understanding the molecular function of other ABBA-containing proteins. But it is already clear that ABBA function includes elements of docking motif, degron motif and regulatory motif.
o 8 selected references:

o 2 Instances for LIG_APCC_ABBAyCdc20_2
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P30283 CLB5
99 105 IVSAVQKRQIYNDRTAAEQE TP 2 Saccharomyces cerevisiae S288c
P47074 MAD3
258 264 SDVNLTKNNVFVDGEESDVE U 1 Saccharomyces cerevisiae (Baker"s yeast)
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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