apc11 (S. pombe, Q9UT86 / SPAC343.03) - review notes

Identity

• Fission-yeast anaphase-promoting complex subunit 11; 94 aa; RING-H2 zinc finger (UniProt ZN_FING 35..78, RING-type); InterPro IPR024991 (RING-H2_APC11), IPR051031 (RING-box E3 ligase family), Pfam PF12861; PANTHER PTHR11210 (RING BOX). Not the S. cerevisiae APC11 (Q12157) nor the pombe SCF RING subunit Rbx1/Pip1 (SPAC23H4.18c), both of which appear as donors in the IBA WITH/FROM lists.
• PomBase product: "anaphase-promoting complex ubiquitin-protein ligase E3 subunit Apc11"; deletion viability: inviable (FYPO:0002061 inviable vegetative cell population; FYPO:0003529 inviable after spore germination, cell-cycle arrest in mitotic interphase, elongated cells; FYPO:0000059 abnormal mitotic cell cycle). The genome-wide deletion set is Kim et al. 2010 PMID:20473289; the apc11-specific result is only in the supplementary tables.
• Inputs used: UniProt record, GOA tsv (18 rows), falcon/Edison deep research (apc11-deep-research-falcon.md), PomBase gene page (API, 2026-09-27), cached publications. Full text in cache: PMID:15060174 (Schwickart 2004), PMID:10888670 (Leverson 2000, budding yeast), PMID:8632802 (Funabiki 1996), PMID:20473289, PMID:26882497. Abstract-only: PMID:12477395 (Yoon 2002), PMID:10651900 (Yanagida 2000 review), PMID:11739784 (Tang 2001, human), PMID:16950791, PMID:18556659. Not cached, cited only through the deep-research file: Ohi et al. 2007 Mol Cell (PMID:18082611, pombe APC/C-Slp1 cryo-EM and stoichiometry), McLean et al. 2011 review (Ubc4/Ubc11 division of labour), Gmachl 2000, Vazquez-Fernandez 2024, Sun 2024.

Founding identification

• Yoon et al. 2002 used TAP + DALPC on the pombe APC/C and brought the subunit count to 13, deliberately capturing small subunits PMID:12477395. Deep research records SPAC343.03 peptides in Lid1-TAP (3) and Apc13-TAP (5) purifications [file:SCHPO/apc11/apc11-deep-research-falcon.md "These data directly connect the exact fission-yeast ORF to the APC/C and support the supplied Q9UT86 annotation."]. UniProt SUBUNIT line cites this paper for the 13-subunit composition including apc11.
• Schwickart et al. 2004 independently purified Cut9-TAP and Apc13-TAP from pombe and recovered the same subunit set [PMID:15060174 "Mass spectrometric analysis of the Cut9-TAP purification identified 10 proteins known or predicted to be APC/C subunits ( 48 )."; "Accordingly, purification of a TAP-tagged version of Apc13 yielded the same set of APC/C subunits as Cut9-TAP (Fig. 2C ), demonstrating that apc13 + encodes a subunit of the fission yeast APC/C."]. Their introduction frames Apc11 correctly [PMID:15060174 "APC/C's RING finger is located within the small subunit Apc11, which by itself has the properties of a minimal ubiquitin ligase ( 13 , 22 )."; "Apc11 is anchored to the complex through Apc2, a subunit distantly related to cullins ( 50 , 54 )."].

Molecular role (conserved RING-E3 mechanism; direct data are from orthologues)

• Budding-yeast Apc11 alone is the minimal ligase PMID:10888670, binds Ubc4 directly PMID:10888670, polyubiquitinates Clb2 PMID:10888670, and the zinc-ligand cysteines are essential PMID:10888670. No thioester intermediate PMID:10888670.
• Human APC2-APC11 is the minimal module and lacks specificity [PMID:11739784 "In combination with Ubc4 or UbcH10, a heterodimeric complex of APC2 and APC11 is sufficient to catalyze the ubiquitination of human securin and cyclin B1."; "However, the minimal APC2/11 ubiquitin ligase module does not possess substrate specificity, because it also ubiquitinates the destruction box deletion mutants of securin and cyclin B1."]. Cullin binding and zinc [PMID:11739784 "Both APC11 and UbcH10 bind to the C-terminal cullin homology domain of APC2, whereas Ubc4 interacts with APC11 directly."; "Zn(2+)-binding and mutagenesis experiments indicate that APC11 binds Zn(2+) at a 1:3 M ratio."].
• Pombe sequence check (UniProt SQ): the Cys/His inventory of the 94-aa protein is H9, C24, C27, C34, C35, C38, C45, C52, H54, H57, H59, C60, C74, i.e. the RING-H2 ligand pattern within the UniProt ZN_FING 35..78 region is intact and the extra cysteines outside the canonical C3H2C3 set match the APC11-family pattern - consistent with the C3H2C3 RING-H2 plus the extra cysteines that form the third zinc site of APC11-family proteins. No residue-level mutagenesis exists for the pombe protein (deep research: "In budding yeast, mutation of zinc-coordinating Apc11 residues disrupted complementation, showing that RING integrity is essential for function").
• Pombe-specific complex biochemistry (via deep research, Yoon 2002 / Ohi 2007): [file:SCHPO/apc11/apc11-deep-research-falcon.md "APC/C ubiquitylated a Cdc2–Cdc13 substrate in an E1-, E2-, and ATP-dependent assay, while cellular APC/C activity generated ubiquitylated Cut2."]; one copy per particle, catalytic side with Apc2 and Apc10 [file:SCHPO/apc11/apc11-deep-research-falcon.md "Apc11, Apc2, and Apc10 occupy the catalytic side of the assembly, spatially separated from much of the TPR scaffold."].
• E2s in fission yeast: Ubc11 (UbcP4) and Ubc4 [file:SCHPO/apc11/apc11-deep-research-falcon.md "Ubc11 can generate short ubiquitin chains in the absence of Ubc4, whereas Ubc4 cannot ubiquitylate APC/C substrates without Ubc11, supporting a model in which Ubc11 participates in initial substrate modification and Ubc4 supports chain extension."]; Leverson 2000 already noted PMID:10888670. Reconstituted pombe APC/C assays use Uba1 + Ubc1/Ubc4/Ubc11 [PMID:26882497 methods]. Chain linkage for pombe not established (deep research: budding yeast K48, human K11).

Biological outputs (pombe)

• Cut2/securin: nuclear, spindle-concentrated, destroyed at anaphase by the Cut9-containing APC/cyclosome; its proteolysis is essential for sister-chromatid separation [PMID:8632802 "Cut2 is located in the nucleus, where it is concentrated along the short metaphase spindle."; "The rapid degradation of Cut2 at anaphase requires its amino-terminal region and the activity of Cut9 (ref. 14), a component of the 20S cyclosome/anaphase-promoting complex (APC), which is necessary for cyclin destruction."; "demonstrating that the regulated proteolysis of Cut2 is essential for sister-chromatid separation."]. Review statement PMID:10651900.
• Cdc13/cyclin B destruction lowers Cdc2 activity for mitotic exit (deep research; Yoon 2002 assay of Cdc2-Cdc13 substrate). Timing of APC/C activity PMID:16950791.
• Specificity comes from coactivators, not Apc11 PMID:18556659. Complex Portal variants: CPX-763 core, CPX-764 (Slp1), CPX-765 (Srw1/Ste9), CPX-766 (Mfr1).
• GO-CAM: PomBase model 67369e7600002505 (mitotic spindle assembly checkpoint signalling) has the APC/C complex (apc11 as a has_part) enabling GO:0061630, part_of GO:0051306 mitotic sister chromatid separation, directly negatively regulating downstream securin and Cdc13 activities (RO:0002630). The module metaphase_anaphase_transition_and_mitotic_exit.yaml lists pombe apc11 as a representative of the APC11 RING unit and is grounded in GO:0007091 and GO:0010458.

Localisation

• No apc11-specific imaging series found [file:SCHPO/apc11/apc11-deep-research-falcon.md "However, the retrieved literature did not provide an Apc11-specific live-cell localization series establishing enrichment at nuclei, spindle-pole bodies, kinetochores, spindles, or chromosomes."]. Nucleus IBA accepted on the basis of closed mitosis, nuclear/spindle Cut2 and nuclear TPR subunits; recorded as a knowledge gap.

Curation decisions (summary)

• All 18 rows ACCEPT. GO:0005680 x5 (IBA, IDA x2, IEA, IPI): defining complex, exact-organism TAP/MS evidence. GO:0061630 x3 (IBA, IEA, TAS): apc11 is the catalytic RING; enables justified because the orthologous RING alone has activity in purified systems. GO:0097602 x2: Apc2 is the cullin-family anchor. GO:0008270 IEA: RING-H2 zinc ligands intact and required for function in orthologues. GO:0016567, GO:0006511, GO:0031145 x2, GO:0045842, GO:1901970: the RING subunit performs the ubiquitination step that these processes name, so participation (not mere necessity) holds.
• GO:0061630 TAS (PMID:10651900): the Yanagida review does not name apc11 in its abstract; kept because the function is clearly correct for the gene, with reference relevance recorded as MEDIUM rather than overruling PomBase.
• GO:1901970 IC: accepted as the pombe-specific formulation of the APC11-node IBA GO:0045842; positive regulation (not GO:0051306 itself) is right because separase, not the APC/C, performs the separation step.
• core_functions include GO:0007091 (module grounding term; pombe apc2 and nuc2 carry it by IBA) - this leaves one validator warning because the APC11 PAINT node used GO:0045842 instead. Not added as NEW: comparator check shows human ANAPC11 and yeast APC11 lack GO:0007091 in GOA and the mixed usage across pombe APC/C subunits (apc2/nuc2 = GO:0007091, cut9/apc11 = GO:0045842) is a representation choice raised under suggested_questions rather than a gap. GO:0010458 exit from mitosis was considered and left out of core_functions (no apc11-specific pombe evidence beyond the deep-research summary of Cdc13 degradation).
• Considered and rejected NEW GO:0031624 ubiquitin conjugating enzyme binding (direct E2 binding shown only for orthologues; no APC11 orthologue carries the term - same comparator result as the yeast APC11 review).
• No protein-binding (GO:0005515) rows, no NOT rows, no isoform rows.