HemN is a cytoplasmic radical-SAM coproporphyrinogen-III dehydrogenase that provides an oxygen-independent route to protoporphyrinogen IX. It binds a catalytic [4Fe-4S] cluster and consumes S-adenosyl-L-methionine while converting two propionate side chains of coproporphyrinogen III to vinyl groups. KT2440 also encodes the oxygen-dependent alternative HemF.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: HemN is catalytic, but this root molecular-function term is uninformative. Reason: GO:0051989 captures the specific radical-SAM coproporphyrinogen dehydrogenase reaction and should replace generic catalytic activity. Proposed replacements: coproporphyrinogen dehydrogenase activity Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt EC=1.3.98.3; |
| GO:0004109 coproporphyrinogen oxidase activity | IEA GO_REF:0000002 | MODIFY | Summary: This describes the pathway position but not HemN's specific radical-SAM chemistry. Reason: The oxygen-independent EC 1.3.98.3 reaction is represented by GO:0051989, whereas GO:0004109 is used for the distinct HemF-type oxidase activity. Proposed replacements: coproporphyrinogen dehydrogenase activity Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt Reaction=coproporphyrinogen III + 2 S-adenosyl-L-methionine = |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Cytoplasmic localization is explicitly predicted for HemN. Reason: UniProt assigns the soluble radical-SAM enzyme to the cytoplasm. Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0006779 porphyrin-containing compound biosynthetic process | IEA GO_REF:0000120 | MODIFY | Summary: The pathway assignment is correct and can be made endpoint-specific for KT2440. Reason: HemN forms protoporphyrinogen IX in the oxygen-independent late route leading to heme B, supporting the live endpoint term GO:0006785. Proposed replacements: heme B biosynthetic process Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt route): step 1/1. |
| GO:0046872 metal ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: This broad metal-binding term is correct but less informative than the cluster term. Reason: HemN's relevant metal center is a defined [4Fe-4S] radical-SAM cluster; generic metal binding remains true but is ancillary to catalysis. Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: This parent is valid but less informative than the specific cluster-type term. Reason: GO:0051539 states the [4Fe-4S] cluster type established for HemN and is preferable as cofactor detail; the broader parent is still correct. Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt Binds 1 [4Fe-4S] cluster. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: A [4Fe-4S] center is integral to radical-SAM catalysis by HemN. Reason: The cofactor assignment is specific and well supported by family-level residue predictions, but the substrate-level dehydrogenase term remains the core molecular function. Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt Binds 1 [4Fe-4S] cluster. |
| GO:0051989 coproporphyrinogen dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the most precise available molecular-function term for HemN. Reason: UniProt assigns EC 1.3.98.3 and RHEA:15425, the radical-SAM conversion of coproporphyrinogen III to protoporphyrinogen IX. Supporting Evidence: file:PSEPK/hemN/hemN-uniprot.txt Reaction=coproporphyrinogen III + 2 S-adenosyl-L-methionine = |
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Download this section (compressed HTML)Q: Is HemN used only under anoxia, or does it contribute under microoxic conditions where HemF is also expressed?
Experiment: Compare hemN and hemF mutant phenotypes across controlled oxygen gradients, including heme-b and pathway-intermediate measurements.
Hypothesis: HemN becomes the principal late-step enzyme when oxygen limits HemF activity.
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