Chloroplastic radical SAM lipoyl synthase that inserts sulfur atoms into octanoylated lipoyl domains to produce protein-bound lipoate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009107 lipoate biosynthetic process | IBA GO_REF:0000033 | MODIFY | Summary: Lipoate biosynthetic process described the core process for LIP1P-2, but GO:0009107 was obsoleted (2026-08-22) in favor of protein lipoylation. Reason: LIP1P-2 catalyzes the sulfur-insertion step of endogenous protein lipoylation; GO:0009107 is now obsolete (replaced_by GO:0009249 protein lipoylation, per GO, obsoleted because term usage was inconsistent), so the annotation should move to the replacement term. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:1934604 · mouse lipoyl synthase Lias SUPPORTS TRANSFER PANTHER:PTN000101947 SUPPORTS TRANSFER Propagation of the lipoate-synthesis role is sound; the MODIFY is ontology maintenance only, because GO:0009107 was obsoleted (2026-08-22) with replaced_by GO:0009249 protein lipoylation. Proposed replacements: protein lipoylation Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt PATHWAY: protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. |
| GO:0016992 lipoate synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: This is the specific core molecular function for this enzyme. Reason: The UniProt entry assigns EC 2.8.1.8 lipoate synthase activity. Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt RecName: Full=Lipoyl synthase; EC=2.8.1.8. |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: Catalytic activity is true but too broad for a characterized lipoyl synthase. Reason: Use the specific lipoate synthase activity term. Proposed replacements: lipoate synthase activity Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt CATALYTIC ACTIVITY: EC=2.8.1.8. |
| GO:0009107 lipoate biosynthetic process | IEA GO_REF:0000120 | MODIFY | Summary: Lipoate biosynthetic process described the core process for LIP1P-2, but GO:0009107 was obsoleted (2026-08-22) in favor of protein lipoylation. Reason: LIP1P-2 catalyzes the sulfur-insertion step of endogenous protein lipoylation; GO:0009107 is now obsolete (replaced_by GO:0009249 protein lipoylation, per GO, obsoleted because term usage was inconsistent), so the annotation should move to the replacement term. Proposed replacements: protein lipoylation Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt PATHWAY: protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. |
| GO:0009249 protein lipoylation | IEA GO_REF:0000104 | ACCEPT | Summary: Protein lipoylation is the direct pathway outcome of lipoyl synthase activity. Reason: The reaction produces protein-bound lipoate on lipoyl domains. Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt FUNCTION: converts octanoylated domains into lipoylated derivatives. |
| GO:0009507 chloroplast | IEA GO_REF:0000120 | ACCEPT | Summary: Chloroplast is the correct localization for this plastidial lipoyl synthase. Reason: The UniProt entry identifies the protein as chloroplastic. Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. |
| GO:0016783 sulfurtransferase activity | IEA GO_REF:0000104 | MODIFY | Summary: Sulfurtransferase activity is broadly correct but less informative than lipoate synthase activity. Reason: The specific radical SAM sulfur insertion reaction is captured by lipoate synthase activity. Proposed replacements: lipoate synthase activity Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt CATALYTIC ACTIVITY: EC=2.8.1.8. |
| GO:0016992 lipoate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the specific core molecular function for this enzyme. Reason: The UniProt entry assigns EC 2.8.1.8 lipoate synthase activity. Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt RecName: Full=Lipoyl synthase; EC=2.8.1.8. |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: Iron-sulfur cluster binding is correct but less specific than 4Fe-4S cluster binding. Reason: The UniProt cofactor annotation specifies two 4Fe-4S clusters. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt COFACTOR: Binds 2 [4Fe-4S] clusters per subunit. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000120 | ACCEPT | Summary: The specific 4Fe-4S cluster binding annotation is supported by UniProt HAMAP curation. Reason: The enzyme requires two 4Fe-4S clusters for radical SAM sulfur insertion. Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt COFACTOR: Binds 2 [4Fe-4S] clusters per subunit. |
| GO:1904047 S-adenosyl-L-methionine binding | IC file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt | NEW | Summary: LIP1P-2 binds S-adenosyl-L-methionine at the unique iron of its radical SAM [4Fe-4S] cluster and cleaves it to the 5'-deoxyadenosyl radical; two SAM are consumed per lipoyl group formed. Reason: Not in GOA. Added under the RADICAL_SAM treatment rule, which treats GO:1904047 as a core cosubstrate-binding function of every radical SAM enzyme whose catalysis is established. This is a molecular function the protein itself performs, so the participation test is met directly: LIP1P-2 binds SAM and cleaves it, rather than merely being required for a process that consumes it. UniProt's curated cofactor note records the exchangeable S-adenosyl-L-methionine on the radical SAM cluster and the entry's binding features name the 4Fe-4S-S-AdoMet ligand, so the claim rests on curated record content rather than on an electronic GO line. Coded IC because the inference is the reviewer's, drawn from that curated content and the established lipoate synthase activity rather than from a SAM-binding assay on this protein. Comparator check, against GOA rather than against this project's own proposals: GOA does annotate GO:1904047 to radical SAM enzymes in exactly this role, by UniRule -- ECOLI/queE (UR000100349), ECOLI/moaA and PSEPK/moaA (UR000101305), METEA/pqqE and PSEPK/pqqE (UR000098303). So the absence here is patchy UniRule coverage, which rules happen to carry the term, not a GO convention against annotating a radical SAM enzyme's own cosubstrate. That is also why those five genes have an existing row to ACCEPT or MODIFY while this one needs a NEW row. Supporting Evidence: file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt Note=Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt cysteines and an exchangeable S-adenosyl-L-methionine file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt /ligand_note="4Fe-4S-S-AdoMet" |
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Download this section (compressed HTML)Q: Do LIP1P-2 and LIP1P-1 differ in expression, plastid targeting efficiency, or substrate preference?
Experiment: Measure isoform-specific rescue of plastid lipoylation defects in transgenic poplar or heterologous plant systems.
Type: targeted functional assay
LIP1P-2-uniprot.txt and GOA provenance.Loading supporting content…
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