CLB2 (P24869) — curation notes

Working journal for the GO annotation review of Saccharomyces cerevisiae CLB2 / YPR119W,
G2/mitotic-specific cyclin-2. Companion to CLB2-ai-review.yaml.

Identity and gestalt

UniProt P24869, 491 aa, cyclin A/B subfamily (IPR046965), two cyclin-box folds (CDD
CYCLIN_CLBs_yeast_rpt1/rpt2). ComplexPortal CPX-1701 "CLB2-CDC28 kinase complex".
Clb2 is not an enzyme. It is the regulatory subunit of Cdc28 (Cdk1); the Clb2-Cdc28
(-Cks1) complex is the dominant M-phase CDK of budding yeast
[file:yeast/CLB2/CLB2-deep-research-falcon.md "Clb2 is not itself an enzyme. Its primary
function is to bind, activate, spatially direct, and confer substrate preference on the
serine/threonine kinase Cdc28/Cdk1."].
Discovery: high-copy suppressor of the mitosis-defective cdc28-1N allele
PMID:1849457; cdc28-1N clb2 is inviable while cdc28-4 clb2 is viable.
Timing: Clb1/Clb2 expressed and activate Cdc28 from late S to mitosis; Clb2 is "the primary
mitotic cyclin" and is absent from meiosis [PMID:8455600 "Clb1 and Clb2 were expressed and
activated p34cdc28 later in the mitotic cell cycle, starting in late S phase and continuing
up to mitosis."; "Clb2, the primary mitotic cyclin in S. cerevisiae, was not detectable
during meiosis."].
All lethal clb deletion combinations include clb2; conditional clb mutants arrest with
duplicated, unseparated SPBs and no spindle [PMID:1387566 "All lethal combinations included
the clb2 deletion, whereas the clb1 clb3 clb4 triple mutant was viable, suggesting a key role
for CLB2."; "Electron microscopy showed that the spindle pole bodies had duplicated but not
separated, and no spindle had formed."].
Mechanistic outputs summarised in the deep research (Chee & Haase 2010 kinesin-5 Kip1/Cin8
phosphosites; Ndd1/Fkh2 positive feedback on the CLB2 cluster; Cdc6 held in a
licensing-incompetent Clb2-Cdk1-Cks1 complex, Philip et al. 2022; Swe1 docking via Clb2
N260/K270, Hu et al. 2008). These PMIDs are not in the local cache, so they are cited only via
the deep-research file.
Inhibition/destruction: Swe1 Y19 phosphorylation (reversed by Mih1), Sic1, Mck1 GSK-3 binding
PMID:22918234, and APC/C-Cdc20 then APC/C-Cdh1 proteolysis PMID:22918234. Clb2 is the
APC/C substrate here, not an actor: no destruction-related process term is proposed
(participation test).

Localization

Primarily nuclear at all stages; bipartite NLS (Srp1/Kap95, Ran), leucine-rich NES, Yrb2
export; NLS deletion increases cytoplasmic and bud-neck signal [PMID:11171327 "Wild-type
Clb2p is primarily nuclear at all points of the cell."; "Deletion of the Clb2p NLS causes
increased cytoplasmic localization of the protein, as well as accumulation at the bud neck."].
Nucleus, mitotic spindle, SPBs and mother-bud neck; neck localization is Clb2-specific and
Bud3-dependent (residues 213-255 + hydrophobic patch), with a cytokinesis delay when lost
PMID:12972503.

Annotation decisions (summary)

Term	Evidence	Action	Note
GO:0000082 G1/S transition	IBA	MARK_AS_OVER_ANNOTATED	deep cyclin node; Clb2 absent in G1, G1/S is Cln/Clb5 territory
GO:0000086 G2/M transition	IMP x2	ACCEPT	core
GO:0000307 CDK holoenzyme complex	IBA	ACCEPT	Clb2-Cdc28-Cks1
GO:0005515 protein binding (Cks1 x3, Cdk substrates x4, Nap1 x3)	IPI	REMOVE	uninformative per policy; interactions not disputed
GO:0005515 protein binding (Mck1)	IPI	MODIFY -> GO:0019901 protein kinase binding	Mck1 is a kinase and binding is the inhibitory mechanism
GO:0005634 nucleus	IBA, IDA x2	ACCEPT
GO:0005737 cytoplasm	IBA, IDA, IMP	ACCEPT	shuttling pool
GO:0005815 MTOC / GO:0005816 SPB / GO:0005819 spindle	IBA/IDA	ACCEPT
GO:0005935 bud neck	IDA	KEEP_AS_NON_CORE	Clb2-specific, peripheral
GO:0006974 DNA damage response	IDA	KEEP_AS_NON_CORE	Clb2-Cdk1 at DSBs phosphorylates Fun30; checkpoint activation
GO:0007089 traversing Start	IBA	MARK_AS_OVER_ANNOTATED	node seeded only by pombe cdc13 (engineered single-cyclin)
GO:0010696 pos. reg. SPB separation	IGI x3	ACCEPT	Kip1/Cin8 phosphorylation is the mechanism
GO:0016538 CDK regulator activity	IBA, IDA, IMP x2, IEA	ACCEPT	regulator term retained on all rows; the more specific GO:0061575 activator activity is used in core_functions (validator notes it is not itself an existing annotation)
GO:0032888 reg. of spindle elongation	IMP	MODIFY -> GO:1902846 positive regulation	direction unambiguous, via Net1/FEAR/Cdc14
GO:0044772 mitotic phase transition	IEA	ACCEPT	broad but correct

Points to revisit

The three Xenopus nap1l1 WITH partners on PMID:7622566 cannot be checked from the cached
abstract; not asserted as mis-attributed, simply uninformative.
DNA damage response: PMID:26801641; clb2Δ has impaired Rad53
phosphorylation and a higher rate of extensive resection. Kept non-core.
Spindle elongation: PMID:23468650.
No NEW terms proposed. Morphogenesis (isotropic growth switch) and cytokinesis timing are
downstream outputs and were not added; a curator may wish to consider
GO:0007117 (budding cell bud growth) only with a direct-substrate argument.