HemF is the cytoplasmic oxygen-dependent coproporphyrinogen-III oxidase. It uses molecular oxygen and a divalent metal cofactor to oxidatively decarboxylate two propionate side chains of coproporphyrinogen III, producing protoporphyrinogen IX. KT2440 also encodes HemN, providing a distinct oxygen-independent alternative for this pathway position.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004109 coproporphyrinogen oxidase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This term captures the oxygen-dependent HemF reaction. Reason: UniProt assigns EC 1.3.3.3 and explicitly describes aerobic oxidative decarboxylation of coproporphyrinogen III to protoporphyrinogen IX. Supporting Evidence: file:PSEPK/hemF/hemF-uniprot.txt Catalyzes the aerobic |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Cytoplasmic localization is explicitly predicted for HemF. Reason: The soluble enzyme has a direct UniProt cytoplasm assignment. Supporting Evidence: file:PSEPK/hemF/hemF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0006779 porphyrin-containing compound biosynthetic process | IEA GO_REF:0000002 | MODIFY | Summary: The pathway assignment is correct and can be made endpoint-specific for KT2440. Reason: HemF forms protoporphyrinogen IX in the oxygen-dependent late route leading to heme B, supporting the live endpoint term GO:0006785. Proposed replacements: heme B biosynthetic process Supporting Evidence: file:PSEPK/hemF/hemF-uniprot.txt route): step 1/1. |
| GO:0006783 heme biosynthetic process | IEA GO_REF:0000104 | ACCEPT | Summary: HemF is a late enzyme in an aerobic realization of heme-b synthesis. Reason: Its protoporphyrinogen IX product is oxidized to protoporphyrin IX and then ferrochelated to heme b. Supporting Evidence: file:PSEPK/hemF/hemF-uniprot.txt FUNCTION: Involved in the heme biosynthesis. |
| GO:0042803 protein homodimerization activity | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Homodimerization is a plausible structural property of HemF. Reason: UniProt predicts a homodimer, but oligomerization is ancillary to the substrate-level oxidase function and should not define the core activity. Supporting Evidence: file:PSEPK/hemF/hemF-uniprot.txt SUBUNIT: Homodimer. |
| GO:0042803 protein homodimerization activity | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: This independent orthology transfer supports the same non-core oligomeric property. Reason: Duplicate evidence is not intrinsically erroneous; both records can be retained as non-core while catalysis remains the defining function. Supporting Evidence: file:PSEPK/hemF/hemF-uniprot.txt SUBUNIT: Homodimer. |
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Download this section (compressed HTML)Q: Under which oxygen ranges does KT2440 switch flux between HemF and HemN?
Experiment: Compare hemF and hemN single and double mutants across oxygen gradients, measuring growth, heme b, and coproporphyrinogen/protoporphyrinogen ratios.
Hypothesis: HemF is the principal coproporphyrinogen oxidase during aerobic growth.
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