ccmC (PA1477, Q9I3N5) notes
Identity
- Heme exporter protein C / cytochrome c-type biogenesis protein CcmC, 252 aa,
six predicted TM helices, CcmC/CycZ/HelC family (TIGR01191, IPR003557,
IPR045062 WWD domain). UniProt PE 3 (homology); function statement is
ECO:0000250 ("Required for the export of heme to the periplasm for the
biogenesis of c-type cytochromes").
- Part of System I cytochrome c maturation (CcmABCDEFGH). CcmC is the
membrane subunit of the CcmA2B1C1(D) ABC-type complex that loads heme onto
the periplasmic heme chaperone CcmE.
Mechanism (E. coli orthologue, P0ABM1)
P. aeruginosa / Pseudomonas genetics
- Baert et al. 2008 (PMID:18174132), the P. aeruginosa ccmC mutant paper:
PMID:18174132
Pleiotropic phenotypes: low pyoverdine, increased pyochelin, reduced
pyocyanin, swarming and twitching motility, rhamnolipid; porphyrin
accumulation; PMID:18174132; reduced [Fe-S]
clusters; complemented by P. fluorescens ccmC.
- P. fluorescens ATCC 17400: ccmC mutant is cytochrome c-deficient and
pyoverdine-deficient; residue substitutions partly separate the two
phenotypes PMID:9822820
- Pyoverdine maturation defect attributed to periplasmic redox:
PMID:12123798
- Catalase defect attributed to heme supply to heme catalases:
PMID:14663086
and PMID:14663086
Reference problem in PseudoCAP rows
All six PseudoCAP IMP rows (catalase activity, pyoverdine biosynthesis,
glycolipid biosynthesis, type IV pilus motility, swimming, swarming; dated
2019-03-11) cite PMID:16824107 (Feissner et al. 2006, Kranz lab). Its
abstract describes biochemistry of the CcmABC complex without naming the
organism; MeSH indexes Escherichia coli and not Pseudomonas, and neither
abstract nor MeSH contains a P. aeruginosa mutant or any of these phenotypes. The phenotypes match,
one for one, the abstract of Baert et al. 2008 (PMID:18174132), the
P. aeruginosa ccmC mutant paper (swimming is not in that abstract; it may be
in the full text). Most likely the PseudoCAP rows were keyed to the wrong
PMID. Neither paper's full text was available here (both abstract-only,
no PMC copy; rechecked 2026-10-29), so the WRONG_REFERENCE defects stay
PROBABLE, not CONFIRMED.
PseudoCAP IBA-seed assessment
| PTN node |
node term |
n_seeds |
leaf IBAs |
seed annotation (term, evidence, PMID) |
verdict |
rationale |
| PTN001247822 |
GO:0004096 catalase activity |
1 (sole seed) |
143 (59 taxa) |
GO:0004096 catalase activity, IMP, PMID:16824107 (PseudoCAP) |
INDIRECT-PHENOTYPE (also WRONG reference) |
CcmC is a 6-TM heme-handling subunit of the Ccm heme-delivery complex with no catalase domain or catalytic residues. The only evidence is loss of catalase activity in the P. aeruginosa ccmC mutant (PMID:18174132, abstract), explained by impaired heme supply to the heme catalases (KatA/KatB). The cited PMID:16824107 is an E. coli Ccm biochemistry paper that does not assay catalase. The seed is unsound, so the IBD and all 143 catalase-activity IBAs from PTN001247822 (including the one back onto ccmC) and the derived IEA "cellular oxidant detoxification" are unsupported and should be withdrawn. |
The same node correctly carries plasma membrane and cytochrome c
biosynthetic process (seeded by E. coli CcmC P0ABM1 and P35162), which are
retained.
Decisions summary
- REMOVE: catalase activity (IMP and IBA), cellular oxidant detoxification
(IEA from catalase), glycolipid biosynthesis (IMP), type IV pilus motility
(IMP), swarming motility (IMP).
- MARK_AS_OVER_ANNOTATED: pyoverdine biosynthesis (IMP; necessity is real,
mechanism unknown and possibly partly separable from cytochrome c), swimming
motility (IMP; not in the abstract, at most an indirect phenotype).
- ACCEPT: plasma membrane (IBA, IEA), heme binding, heme transmembrane
transporter activity, heme transport, cytochrome c biosynthetic process.
- MODIFY: membrane -> plasma membrane; cytochrome complex assembly ->
cytochrome c biosynthetic process.