CPR4 (S. cerevisiae, YCR069W, P25334) — curation notes

Journal of research for the AI GO-annotation review. Inline provenance uses
[PMID:xxxx "verbatim supporting text"].

Identity (verified)

CPR4 is one of eight cyclophilins in S. cerevisiae (CPR1–CPR8). Its closest paralog is
CPR8 (P53728, CYP8); both are the yeast "cyclophilin C (CypC)"-type / vacuolar cyclophilins
and share PANTHER subfamily SF568 (verified in
interpro/panther/PTHR11071/PTHR11071-entries.csv: both P25334/CPR4 and P53728/CPR8 map to
SF568 "CPR4-RELATED"). PMID:15998457. Dolinski et al. describe Cpr8 as
"a homolog of the secretory pathway cyclophilin Cpr4" PMID:9371805.

Domain architecture (verified from UniProt FT + inline sequence analysis)

Franco et al. 1991 described exactly this dual topology from sequence:
PMID:1803821 and concluded PMID:1803821. UniProt SUBCELLULAR LOCATION: "Membrane; Single-pass
membrane protein" (ECO:0000305, an inference, not experimental).

Catalytic-residue / CsA-pocket analysis (inline, this review)

I compared the CPR4 cyclophilin domain to human cyclophilin A (PPIA, P62937), whose
catalytic/CsA-contact residues are well established.

Catalytic core motifs are PRESENT and correctly positioned within the 55–225 domain:
NNFAML (pos 82), HTYSYR (104), GPFTVYGP (132), FGPD (161), GQITSG (190), RFLYFV (219).
These correspond to conserved cyclophilin catalytic/substrate-binding elements → PPIase
catalytic machinery is intact → PPIase (GO:0003755) is domain-defensible.

NOTABLE DIVERGENCE — the conserved CsA-binding tryptophan is ABSENT.
Human CypA has a single Trp, W121, in FICTAKTEWLDGKHVV; W121 lines the cyclosporin-A
pocket and is a key CsA contact. The homologous region in CPR4 is IITTKADGNEELDGK —
no Trp in the entire cyclophilin domain (the protein's only Trp is W2, in the signal peptide).
Whole-domain Trp count = 0. This is independently corroborated by Franco et al. as reported
in the deep-research synthesis: the W121-equivalent is replaced by glutamate in Scc3/CPR4
(a W121E-type substitution) [file:yeast/CPR4/CPR4-deep-research-falcon.md, citing Franco 1991].
Interpretation: CPR4 likely has reduced/altered cyclosporin-A binding relative to canonical
cyclophilins, even though the PPIase catalytic residues are conserved. In human CypA, W121→F/A
lowers CsA affinity 75–200-fold but PPIase activity only 2–13-fold, showing the two are
structurally separable. (This is a sequence-based prediction; CPR4 CsA binding is untested.)

NinaA structural parallel (functional hypothesis, not established for CPR4)

The only cyclophilin sharing CPR4's dual topology (N-terminal signal peptide + C-terminal TM +
central CLD) is Drosophila NinaA, a membrane-anchored, secretory-pathway cyclophilin
required for correct folding and ER→Golgi transport of rhodopsin. Franco 1991
PMID:1803821 and PMID:1803821. NinaA is a CypC ortholog PMID:15998457. This motivates a hypothesis that CPR4 is a
membrane-anchored, substrate-specific foldase for secretory/membrane clients — but yeast has no
rhodopsins and CPR4's substrates are unknown.

What is KNOWN vs NOT known about CPR4 specifically

KNOWN (or well-supported)

  1. CPR4 is a cyclophilin-family PPIase by sequence/homology (UniProt, PANTHER, InterPro,
    Pfam PF00160, CDD cd00317). Catalytic residues intact (this review). EC 5.2.1.8.
  2. Signal peptide + C-terminal TM helix → a secretory-pathway / ER, membrane cyclophilin
    [PMID:1803821; PMID:15998457]. Dolinski et al. call it "the secretory pathway cyclophilin
    Cpr4" PMID:9371805.
  3. CPR4 is non-essential. None of the eight yeast cyclophilins (nor an octuple mutant) is
    essential; little/no functional redundancy [PMID:15998457 "none of the eight individual
    cyclophilins was found to be essential in S. cerevisiae"; "an octuplet mutant lacking all
    eight cyclophilins was viable and that there was little or no evidence for functional
    redundancy"]; corroborated for all 12 immunophilins in [PMID:9371805 "None of the eight
    cyclophilins or four FKBPs were essential"; "yeast mutants lacking all 12 immunophilins were
    viable"].
  4. Localization: Wang & Heitman 2005 place Cpr4 (and Cpr8) in vacuoles PMID:15998457. SGD HDA (systematic microscopy) also assigns
    the fungal-type vacuole (GO:0000324) [PMID:26928762 source dataset]. Family-level IBA instead
    assigns ER (GO:0005783)/cytoplasm. So localization data are partly discordant (vacuole vs ER);
    both are within the secretory/endomembrane system and not mutually exclusive for a protein
    that transits the ER en route to the vacuole. PMID:26928762 is a genome-wide library/methods
    paper and does not discuss CPR4 individually.

NOT known (genuine gaps)

Annotation-by-annotation plan (8 GOA rows)

  1. GO:0003755 PPIase, IBA (GO_REF:0000033), enables → ACCEPT (core MF; catalytic residues intact).
  2. GO:0005783 endoplasmic reticulum, IBA, is_active_in → KEEP_AS_NON_CORE: architecture
    (signal peptide + TM) supports secretory/ER; note vacuole is the more specific experimental call.
  3. GO:0006457 protein folding, IBA, involved_in → ACCEPT as general family-level BP; no
    CPR4-specific in-vivo process known → keep general.
  4. GO:0003755 PPIase, IEA (GO_REF:0000120 InterPro/EC), enables → ACCEPT (redundant MF confirmation).
  5. GO:0016020 membrane, IEA (GO_REF:0000044 SubCell), located_in → KEEP_AS_NON_CORE:
    C-terminal TM helix supports membrane; general term.
  6. GO:0000324 fungal-type vacuole, HDA (PMID:26928762), located_in → KEEP_AS_NON_CORE
    (experimental localization; concordant with Wang&Heitman vacuole; do not remove).
  7. GO:0003755 PPIase, ISS (PMID:9371805), enables → ACCEPT (ISS from a cyclophilin homolog; MF consistent).
  8. GO:0008150 biological_process (root), ND (GO_REF:0000015) → ACCEPT (honest "no specific BP known" placeholder).

References