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 six amino acids. It was named ‘ABBA motif’ since it was originally identified in A-type cyclins, Bub1, BubR1 and yeast Acm1. The motif occupies a hydrophobic groove between blades 2 and 3 on the opposite surface of the WD40 domain from the KEN box binding pocket. ABBA positions 1 and 3 are deeply buried, position 4 rests against blade 3, and position 6 reaches out of the pocket to contact the side of the WD40 repeat, while positions 2 and 5 contain flexible residues which point away from the binding pocket (He,2013).
The ABBA motif that binds to the metazoan Cdc20 and fungal Cdh1 starts with a hydrophobic residue from the set [ILVMF]. The P3 position prefers an I/V/L, however a conserved substitution of proline is observed at this position on the second ABBA motif of ABBA-KEN-ABBA cassette. The P4 position strongly favours an aromatic residue and is followed by negatively charged amino acids at the P6 position. The key residues in the ABBA binding pocket of human Cdc20 and yeast Cdh1/Cdc20 are conserved enough to accommodate a typical ABBA motif. But the metazoan Cdh1 has a diverged sequence at the key positions in the ABBA motif binding pocket and it no longer binds to an ABBA motif. In yeast Cdh1, the ABBA motif binding pocket is largely conserved relative to the human Cdc20 binding pocket but the fungal Cdc20 binding pocket is slightly diverged and it recognizes a different motif having preference for two basic residues at the initial positions instead of a hydrophobic residue present in the metazoan instances. In almost all eukaryotic lineages, an evolutionarily conserved ABBA-KEN-ABBA cassette is found in the BubR1 protein with a constrained inter-motif distance despite the large evolutionary distances (Di Fiore et al., in press, 2016 ). The metazoan cyclin A acquired the ABBA motif independently of the yeast cyclin Clb5, although both order the mitotic cyclin's degradation, and so this is an example of convergent evolution (Davey,2016).
Pattern: [ILVMF].[ILMVP][FHY].[DE]
Pattern Probability: 0.0003843
Present in taxon: Eukaryota
Interaction Domain:
WD40 (PF00400) WD domain, G-beta repeat (Stochiometry: 2 : 1)
o See 11 Instances for LIG_APCC_ABBA_1
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 10 GO-Terms:

o 11 Instances for LIG_APCC_ABBA_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P47074 MAD3
331 336 KRPYDEKLPIFRDSIGRSDP U 1 Saccharomyces cerevisiae (Baker"s yeast)
O60566 BUB1B
340 345 VPAVLPSFTPYVEETARQPV TP 3 Homo sapiens (Human)
O60566 BUB1B
272 277 QMQNNSRITVFDENADEAST TP 3 Homo sapiens (Human)
1114 1119 LDDDKRQLRLYQERYLADGD FP 1 Homo sapiens (Human)
O60566 BUB1B
528 533 SKGPSVPFSIFDEFLLSEKK TP 9 Homo sapiens (Human)
953 958 SPQYACDFNLFLEDSADNRQ FP 1 Homo sapiens (Human)
Q14674 ESPL1
1362 1367 QAGPHVPFTVFEEVCPTESK FP 1 Homo sapiens (Human)
O43683 BUB1
527 532 ISSLSSAFHVFEDGNKENYG TP 3 Homo sapiens (Human)
P20248 CCNA2
99 104 ANSKQPAFTIHVDEAEKEAQ TP 3 Homo sapiens (Human)
P78396 CCNA1
135 140 QEPPKQGFDIYMDELEQGDR TP 3 Homo sapiens (Human)
Q08981 ACM1
61 66 QISKAAQFMLYEETAEERNI TP 10 Saccharomyces cerevisiae S288c
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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