CcmF (PA1480) is a polytopic inner-membrane protein of the System I cytochrome c maturation (Ccm) pathway. Together with CcmH it forms the heme lyase (holocytochrome c synthase) that takes heme from the periplasmic chaperone holo-CcmE and attaches it covalently to the CXXCH motifs of apocytochromes c in the periplasm. CcmF belongs to the CcmF/CycK/Ccl1/NrfE/CcsA family; in the E. coli orthologue it carries a b-type heme ligated by conserved transmembrane histidines and acts in vitro as a quinol:heme oxidoreductase, thought to keep the heme reduced for attachment. In P. aeruginosa a ccmF insertion mutant shows milder versions of the pleiotropic defects of a ccmC mutant, including reduced [Fe-S] cluster content.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | MARK AS OVER ANNOTATED | Summary: Pyoverdine production is reduced in ccm mutants, most strongly ccmC and less so ccmF. CcmF does no step of pyoverdine synthesis; the cited PMID also appears to be the wrong paper. Reason: Treated as for ccmC (genes/PSEAE/ccmC). The pyoverdine defect of ccm mutants is attributed to the loss of periplasmic oxidising power that c-type cytochromes provide for ferribactin maturation; it shows that ccmF is necessary, not that CcmF participates. The abstract of the likely source (PMID:18174132) reports the pyoverdine defect mainly for ccmC, and only says that ccmF had a range of milder changes, so whether the ccmF mutant itself was assayed for pyoverdine cannot be read from it. Marked over-annotated rather than removed because the evidence behind the row could not be seen. Supporting Evidence: PMID:18174132 The ccmC mutant, and to a lesser extent the ccmF mutant, showed a range of other phenotypic changes. PMID:18174132 The production of the siderophore pyoverdine was very low and growth under the condition of iron limitation was severely restricted |
| GO:0004096 catalase activity | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | REMOVE | Summary: Seed row for the oxidoreductase IBD at PTN009171456. CcmF is not a catalase; loss of catalase activity in ccm mutants reflects poor heme supply to the heme catalases. Reason: A molecular function asserted from loss of an enzyme activity in a mutant is an indirect phenotype. P. aeruginosa catalases (KatA, KatB, KatE) are separate heme enzymes; CcmF is a membrane heme-lyase subunit with no catalase domain. The abstract of the likely source attributes undetectable catalase to the ccmC mutant; for ccmF nothing is stated. The same row was removed on ccmC (CONFIRMED there). As a seed of PTN009171456 (GO:0016491 oxidoreductase activity), the row is unsound, but the IBD stands on E. coli CcmF (P33927), which has direct quinol:heme oxidoreductase evidence. Supporting Evidence: PMID:18174132 The ccmC mutant was also found to accumulate porphyrins, and catalase production was undetectable, consistent with the increased sensitivity to hydrogen peroxide. PMID:19629033 CcmF, shown to have 13 TMDs, is therefore a cytochrome b , and we show that it acts in vitro as a quinol:haem oxidoreductase |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Inner (plasma) membrane location; IBD seeded by E. coli CcmF and NrfE, sound. Reason: CcmF is a polytopic inner-membrane protein with many predicted TM helices; the seeds have experimental inner-membrane locations. Supporting Evidence: file:PSEAE/ccmF/ccmF-uniprot.txt TRANSMEM 8..28 PMID:19629033 CcmF, shown to have 13 TMDs, is therefore a cytochrome b , and we show that it acts in vitro as a quinol:haem oxidoreductase |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Cell inner membrane, from UniProt subcellular location. Reason: Consistent with topology and the IBA row. Supporting Evidence: file:PSEAE/ccmF/ccmF-uniprot.txt TRANSMEM 8..28 |
| GO:0015232 heme transmembrane transporter activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: CcmF receives heme from holo-CcmE in the periplasm and attaches it to apocytochrome; it is not shown to move heme across the membrane. Reason: The InterPro2GO mapping from the cytochrome c biogenesis family signatures applies heme transmembrane transport, which fits the CcsBA (System II) members of the family that export heme. In System I, heme is exported by CcmABCD and delivered by CcmE; CcmF takes heme from holo-CcmE and catalyses attachment. A transport role for CcmF is not established, so the term over-states its function. Supporting Evidence: PMID:19629033 Given the published interaction of holoCcmE with CcmF file:PSEAE/ccmF/ccmF-uniprot.txt Required for the biogenesis of c-type cytochromes. Possible subunit of a heme lyase (By similarity). PMID:16824107 This ABC transporter is composed of the ABC subunit CcmA, and two membrane proteins, CcmB and CcmC. |
| GO:0015886 heme transport | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: CcmF takes part in heme trafficking from CcmE to apocytochrome c; heme transport in the broad sense is acceptable but peripheral to the lyase function. Reason: CcmF accepts heme from holo-CcmE and hands it to apocytochromes, a step of the heme trafficking pathway of System I. The core role is covalent heme attachment (cytochrome c-heme linkage). Supporting Evidence: PMID:19629033 Given the published interaction of holoCcmE with CcmF PMID:19629033 A completely conserved histidine in TMD5 of CcmF is an axial ligand to this haem, suggesting a conserved quinol-mediated mechanism to reduce the haem for covalent attachment |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Correct but general; CcmF is in the plasma (inner) membrane. Reason: The gene already carries plasma membrane (IBA, IEA), supported by its topology. Proposed replacements: plasma membrane Supporting Evidence: file:PSEAE/ccmF/ccmF-uniprot.txt TRANSMEM 8..28 |
| GO:0016491 oxidoreductase activity | IBA GO_REF:0000033 | MODIFY | Summary: CcmF orthologues carry a b-heme and act as quinol:heme oxidoreductases; the IBA is correct for CcmF, though its PseudoCAP seed (catalase) is not. The specific supported activity is oxidoreductase acting on diphenols (quinols). Reason: The IBD at PTN009171456 has two seeds, P. aeruginosa CcmF (PseudoCAP catalase IMP, unsound) and E. coli CcmF (P33927), which carries GO:0016679 oxidoreductase activity, acting on diphenols and related substances as donors (IDA, PMID:19629033). The IBD therefore stands without the PseudoCAP seed. The general term is correct but less specific than the evidence: quinols are diphenols, and E. coli CcmF reduces its b-heme with quinols in vitro. The heme-ligating histidines are completely conserved, so the activity is expected in P. aeruginosa CcmF. Refined to GO:0016679. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN009171456 · PTN009171456 SUPPORTS TRANSFER CcmF clade node (67 leaves, 36 taxa). The node term is generic but correct; E. coli CcmF experimental evidence supports a quinol:heme oxidoreductase. UniProtKB:P33927 · E. coli CcmF SUPPORTS TRANSFER IDA GO:0016679 (PMID:19629033), quinol reduction of the CcmF b-heme in vitro. UniProtKB:Q9I3N2 · ccmF (PA1480) SOURCE BAD The seed is a PseudoCAP catalase IMP row recording a mutant phenotype, keyed to a paper (PMID:16824107) that does not concern CcmF. Proposed replacements: oxidoreductase activity, acting on diphenols and related substances as donors Supporting Evidence: PMID:19629033 CcmF, shown to have 13 TMDs, is therefore a cytochrome b , and we show that it acts in vitro as a quinol:haem oxidoreductase PMID:19629033 A completely conserved histidine in TMD5 of CcmF is an axial ligand to this haem, suggesting a conserved quinol-mediated mechanism to reduce the haem for covalent attachment |
| GO:0017004 cytochrome complex assembly | IEA GO_REF:0000002 | MODIFY | Summary: CcmF acts in covalent heme attachment to apocytochromes c, not in assembly of a multi-subunit cytochrome complex. Reason: GO:0018063 cytochrome c-heme linkage is a descendant of GO:0017004 and is the process the CcmFH heme lyase carries out; it is the term E. coli CcmF carries from experimental evidence. Proposed replacements: cytochrome c-heme linkage Supporting Evidence: file:PSEAE/ccmF/ccmF-uniprot.txt Required for the biogenesis of c-type cytochromes. Possible subunit of a heme lyase (By similarity). PMID:19629033 A completely conserved histidine in TMD5 of CcmF is an axial ligand to this haem, suggesting a conserved quinol-mediated mechanism to reduce the haem for covalent attachment |
| GO:0020037 heme binding | IEA GO_REF:0000002 | ACCEPT | Summary: CcmF binds a b-type heme through conserved transmembrane histidines (shown for E. coli CcmF) and handles the heme donated by CcmE. Reason: Heme binding is well established for the orthologue, and P. aeruginosa CcmF has the same family domains (PF01578, CcmF_C). Supporting Evidence: PMID:19629033 CcmF, shown to have 13 TMDs, is therefore a cytochrome b , and we show that it acts in vitro as a quinol:haem oxidoreductase PMID:19629033 A completely conserved histidine in TMD5 of CcmF is an axial ligand to this haem, suggesting a conserved quinol-mediated mechanism to reduce the haem for covalent attachment file:PSEAE/ccmF/ccmF-uniprot.txt PF01578; Cytochrom_C_asm; 1. |
| GO:0043107 type IV pilus-dependent motility | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | REMOVE | Summary: Reduced twitching in ccm mutants is a pleiotropic consequence of losing cytochrome c maturation; CcmF is not a pilus component. Reason: The likely source paper lists twitching among traits secondarily affected by ccm mutation (most strongly ccmC). CcmF does no part of type IV pilus-dependent motility. Removed, as on ccmC; the cited PMID also appears to be wrong. Supporting Evidence: PMID:18174132 Interestingly, other traits were also strongly affected by the ccmC mutation, including the production of pyocyanin, swarming and twitching motility, and rhamnolipid production. PMID:18174132 The ccmC mutant, and to a lesser extent the ccmF mutant, showed a range of other phenotypic changes. |
| GO:0071977 bacterial-type flagellum-dependent swimming motility | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | MARK AS OVER ANNOTATED | Summary: Swimming is not among the phenotypes in either abstract; any swimming defect of a ccmF mutant would be an indirect energetic phenotype. Reason: As for ccmC: a swimming phenotype may be in the full text of PMID:18174132, which could not be read, but a motility defect in a cytochrome c maturation mutant is a pleiotropic consequence, not participation in flagellar motility. Marked over-annotated rather than removed because the evidence behind the row could not be seen. Supporting Evidence: PMID:18174132 The ccmC mutant, and to a lesser extent the ccmF mutant, showed a range of other phenotypic changes. |
| GO:0071978 bacterial-type flagellum-dependent swarming motility | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | REMOVE | Summary: Reduced swarming in ccm mutants is a pleiotropic phenotype (swarming also needs rhamnolipid, reduced in these mutants). Reason: CcmF is not a flagellar or motility component. The likely source abstract groups swarming with pyocyanin, twitching and rhamnolipid as secondarily affected traits. Removed, as on ccmC. Supporting Evidence: PMID:18174132 Interestingly, other traits were also strongly affected by the ccmC mutation, including the production of pyocyanin, swarming and twitching motility, and rhamnolipid production. |
| GO:0098869 cellular oxidant detoxification | IEA GO_REF:0000108 | REMOVE | Summary: Inferred automatically from the catalase activity row, which is an indirect phenotype and is removed. Reason: This GO_REF:0000108 inference rests entirely on GO:0004096 catalase activity (PseudoCAP IMP), removed here. CcmF does not detoxify oxidants. Supporting Evidence: file:PSEAE/ccmF/ccmF-uniprot.txt Required for the biogenesis of c-type cytochromes. Possible subunit of a heme lyase (By similarity). |
Loading supporting content…
Download this section (compressed HTML)Q: Should System I CcmF(H) carry GO:0004408 holocytochrome-c synthase activity, as eukaryotic HCCS does, given that it catalyses covalent heme attachment to apocytochrome c?
Experiment: Measure c-type cytochrome content and pyoverdine production in a P. aeruginosa ccmF deletion complemented with CcmF variants lacking the conserved TM histidine heme ligands, to test whether the b-heme redox centre is needed in vivo.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)