Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003824 catalytic activity	IEA GO_REF:0000002	MODIFY	Summary: IEA from InterPro IPR004821 (cytidylyltransferase-like domain). Correct but uninformative; the specific activity is pantetheine-phosphate adenylyltransferase. Proposed replacements: pantetheine-phosphate adenylyltransferase activity Supporting Evidence: file:yeast/CAB4/CAB4-uniprot.txt Reaction=(R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA +
GO:0004140 dephospho-CoA kinase activity	IBA GO_REF:0000033	REMOVE	Summary: IBA from PANTHER PTN000075336 (dephospho-CoA kinase node; donors E. coli CoaE P0A6I9, mouse Coasy, Arabidopsis DPCK). Cab4 shares the PANTHER family PTHR10695 with COASY because mammalian COASY fuses PPAT and DPCK domains, but Cab4 contains only the cytidylyltransferase-like PPAT domain (IPR004821) and no CoaE/DPCK domain (IPR001977). In yeast DPCK activity is provided by the separate gene CAB5 (CoaE family). The propagation to Cab4 is a domain-architecture error. Reason: Cab4 lacks the dephospho-CoA kinase domain; the activity belongs to Cab5. IBA propagated across a fused (COASY-type) family to a single-domain PPAT. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000075336 · PTN000075336 SUPPORTS SOURCE BUT NOT TARGET The node is seeded by dephospho-CoA kinases (E. coli CoaE, the DPCK domain of mouse Coasy, Arabidopsis DPCK). Cab4 is a single-domain eukaryotic CoaD-family PPAT (only IPR004821 cytidylyltransferase-like domain) that corresponds to the PPAT half of COASY; the yeast DPCK is the separate CoaE-family protein Cab5. Supporting Evidence: file:yeast/CAB4/CAB4-uniprot.txt DR InterPro; IPR004821; Cyt_trans-like. file:yeast/CAB4/CAB4-uniprot.txt SIMILARITY: Belongs to the eukaryotic CoaD family. {ECO:0000305}. PMID:19266201 Null mutants could be complemented by their bacterial counterparts coaBC, coaD and coaE, respectively.
GO:0004595 pantetheine-phosphate adenylyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: IEA via RHEA:19801 / EC 2.7.7.3. Correct; core MF. Supporting Evidence: file:yeast/CAB4/CAB4-uniprot.txt Reaction=(R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA +
GO:0004595 pantetheine-phosphate adenylyltransferase activity	ISS PMID:11923312 Complete reconstitution of the human coenzyme A biosynthetic...	ACCEPT	Summary: ISS from human COASY (Q13057) PPAT domain characterised by Daugherty et al. 2002. Cab4 is homologous to the COASY PPAT domain; the null is complemented by E. coli coaD, supporting PPAT activity. Supporting Evidence: PMID:11923312 Using comparative genomics, we have identified human genes encoding the last four enzymatic steps in CoA biosynthesis PMID:19266201 Null mutants could be complemented by their bacterial counterparts coaBC, coaD and coaE, respectively.
GO:0004595 pantetheine-phosphate adenylyltransferase activity	RCA GO_REF:0000123	ACCEPT	Summary: RCA from YeastPathways PANTOSYN2-PWY assigning Cab4 to 4'-phosphopantetheine + ATP -> 3'-dephospho-CoA + PPi (EC 2.7.7.3). Correct. Supporting Evidence: file:yeast/CAB4/CAB4-uniprot.txt Reaction=(R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA +
GO:0005515 protein binding	IPI PMID:23789928 Molecular characterization of the heteromeric coenzyme A-syn...	REMOVE	Summary: IPI with Cab3 (P36076) (Olzhausen et al. 2013). 'Protein binding' conveys no functional information; the biologically meaningful content of Cab-protein interactions is captured by CoA-synthesizing protein complex (GO:1990143) / PPCDC complex (GO:0071513) membership. Reason: Uninformative 'protein binding' term; interaction is not disputed but is better represented by complex membership.
GO:0005515 protein binding	IPI PMID:23789928 Molecular characterization of the heteromeric coenzyme A-syn...	REMOVE	Summary: IPI with Cab2 (P40506) (Olzhausen et al. 2013). 'Protein binding' conveys no functional information; the biologically meaningful content of Cab-protein interactions is captured by CoA-synthesizing protein complex (GO:1990143) / PPCDC complex (GO:0071513) membership. Reason: Uninformative 'protein binding' term; interaction is not disputed but is better represented by complex membership.
GO:0005515 protein binding	IPI PMID:23789928 Molecular characterization of the heteromeric coenzyme A-syn...	REMOVE	Summary: IPI with Cab5 (Q03941) (Olzhausen et al. 2013). 'Protein binding' conveys no functional information; the biologically meaningful content of Cab-protein interactions is captured by CoA-synthesizing protein complex (GO:1990143) / PPCDC complex (GO:0071513) membership. Reason: Uninformative 'protein binding' term; interaction is not disputed but is better represented by complex membership.
GO:0005634 nucleus	HDA PMID:14690591 Assigning function to yeast proteins by integration of techn...	KEEP AS NON CORE	Summary: HDA (Hazbun et al. 2003 essential-ORF imaging). No nuclear function known. Reason: High-throughput observation without functional support. Supporting Evidence: PMID:14690591 fluorescence microscopy to localize the proteins
GO:0005634 nucleus	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: IEA from UniProt subcellular location (Nucleus, from Hazbun et al. 2003). Same basis. Reason: High-throughput localisation only.
GO:0005737 cytoplasm	HDA PMID:14690591 Assigning function to yeast proteins by integration of techn...	ACCEPT	Summary: HDA (Hazbun et al. 2003). Consistent with membership of the soluble CoA-SPC. Supporting Evidence: PMID:14690591 fluorescence microscopy to localize the proteins
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: IEA from UniProt subcellular location (Cytoplasm). Correct.
GO:0005829 cytosol	RCA GO_REF:0000123	ACCEPT	Summary: RCA from YeastPathways PANTOSYN2-PWY (cytosolic step). Consistent.
GO:0015937 coenzyme A biosynthetic process	IBA GO_REF:0000033	ACCEPT	Summary: IBA (PTN000075336) for CoA biosynthesis. Although the DPCK MF propagated from this node is wrong for Cab4, involvement in CoA biosynthesis is correct (PPAT is step 4/5). Supporting Evidence: PMID:19266201 Similar to CAB1, genes YIL083C, YKL088W, YGR277C and YDR106C responsible for late CoA biosynthesis turned out as essential.
GO:0015937 coenzyme A biosynthetic process	IGI PMID:19266201 Genetic analysis of coenzyme A biosynthesis in the yeast Sac...	ACCEPT	Summary: IGI (Olzhausen et al. 2009) with E. coli coaD (P0A6I6): the bacterial PPAT complements the essential YGR277C null. Supporting Evidence: PMID:19266201 Similar to CAB1, genes YIL083C, YKL088W, YGR277C and YDR106C responsible for late CoA biosynthesis turned out as essential. PMID:19266201 Null mutants could be complemented by their bacterial counterparts coaBC, coaD and coaE, respectively.
GO:0015937 coenzyme A biosynthetic process	ISS PMID:11923312 Complete reconstitution of the human coenzyme A biosynthetic...	ACCEPT	Summary: ISS from human COASY (Daugherty et al. 2002). Correct. Supporting Evidence: PMID:11923312 Using comparative genomics, we have identified human genes encoding the last four enzymatic steps in CoA biosynthesis
GO:0015937 coenzyme A biosynthetic process	NAS PMID:19266201 Genetic analysis of coenzyme A biosynthesis in the yeast Sac...	ACCEPT	Summary: NAS (Olzhausen et al. 2009). Correct; redundant. Supporting Evidence: PMID:19266201 Similar to CAB1, genes YIL083C, YKL088W, YGR277C and YDR106C responsible for late CoA biosynthesis turned out as essential.
GO:0015937 coenzyme A biosynthetic process	RCA GO_REF:0000123	ACCEPT	Summary: RCA from YeastPathways PANTOSYN2-PWY. Correct.
GO:1990143 CoA-synthesizing protein complex	IDA PMID:23789928 Molecular characterization of the heteromeric coenzyme A-syn...	ACCEPT	Summary: IDA (Olzhausen et al. 2013): Cab4 binds Cab2, Cab3 and Cab5 in the CoA-synthesizing protein complex. Supporting Evidence: PMID:23789928 Our results show that Cab2, Cab3, Cab4, and Cab5 indeed bind to each other, with Cab3 as the sole protein, which can interact with itself and other Cab proteins. PMID:23789928 Our interaction studies confirm early reports on the existence of a CoA-synthesizing protein complex (CoA-SPC) in yeast
GO:1990143 CoA-synthesizing protein complex	NAS PMID:23789928 Molecular characterization of the heteromeric coenzyme A-syn...	ACCEPT	Summary: NAS (Olzhausen et al. 2013). Correct; redundant. Supporting Evidence: PMID:23789928 Our interaction studies confirm early reports on the existence of a CoA-synthesizing protein complex (CoA-SPC) in yeast

Core Functions

Phosphopantetheine adenylyltransferase: ATP-dependent adenylylation of 4'-phosphopantetheine to 3'-dephospho-CoA (step 4 of CoA biosynthesis), as a component of the cytosolic CoA-SPC; monofunctional, unlike mammalian COASY.

Molecular Function:

pantetheine-phosphate adenylyltransferase activity

Directly Involved In:

coenzyme A biosynthetic process

Cellular Locations:

cytosol

In Complex:

CoA-synthesizing protein complex

Supporting Evidence:

file:yeast/CAB4/CAB4-uniprot.txt
Reaction=(R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA +
PMID:19266201
Null mutants could be complemented by their bacterial counterparts coaBC, coaD and coaE, respectively.
PMID:11923312
Using comparative genomics, we have identified human genes encoding the last four enzymatic steps in CoA biosynthesis
PMID:23789928
Our results show that Cab2, Cab3, Cab4, and Cab5 indeed bind to each other, with Cab3 as the sole protein, which can interact with itself and other Cab proteins.

References

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Suggested Experiments

Experiment: Purify Cab4 and measure PPAT activity directly (no direct biochemical assay of the yeast enzyme is cached); confirm absence of dephospho-CoA kinase activity.

Deep Research

SGD

(CAB4-deep-research-sgd.md)

SGD gene description for CAB4 (yeast) SGD

SGD gene description for CAB4 (yeast)

Subunit of the CoA-Synthesizing Protein Complex (CoA-SPC); subunits of this complex are: Cab2p, Cab3p, Cab4p, Cab5p, Sis2p and Vhs3p; involved in histone acylation; probable pantetheine-phosphate adenylyltransferase (PPAT); PPAT catalyzes the fourth step in the biosynthesis of coenzyme A from pantothenate; null mutant lethality is complemented by E. coli coaD (encoding PPAT) and by human COASY

📚 Additional Documentation

Notes

(CAB4-notes.md)

CAB4 (YGR277C, P53332) notes

Eukaryotic CoaD-family PPAT, single domain [UniProt:P53332 "Belongs to the eukaryotic CoaD family."; InterPro IPR004821 only]
Complemented by E. coli coaD PMID:19266201
Human ortholog domain = PPAT half of COASY PMID:11923312
CoA-SPC member PMID:23789928

Key finding: IBA GO:0004140 dephospho-CoA kinase activity (PTN000075336) is a mis-propagation - Cab4 has no CoaE/DPCK domain; yeast DPCK is CAB5. REMOVE with propagation_review. No direct biochemical PPAT assay of yeast Cab4 is cached.

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