Existing Annotations Review

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.

Core Functions

Catalyzes the chloroplast lipoyl synthase reaction, converting octanoylated protein domains into lipoylated derivatives during lipoate biosynthesis and protein lipoylation.

Molecular Function:

lipoate synthase activity

Directly Involved In:

protein lipoylation

Cellular Locations:

chloroplast

Supporting Evidence:

file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt
FUNCTION: Catalyzes the radical-mediated insertion of two sulfur atoms into the octanoyl moiety bound to lipoyl domains.
file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt
CATALYTIC ACTIVITY: EC=2.8.1.8.
file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt
SUBCELLULAR LOCATION: Plastid, chloroplast.

References

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Suggested Experiments

Experiment: Measure isoform-specific rescue of plastid lipoylation defects in transgenic poplar or heterologous plant systems.

Type: targeted functional assay

📚 Additional Documentation

Notes

(LIP1P-2-notes.md)

LIP1P-2 notes

Reviewed existing GOA annotations against LIP1P-2-uniprot.txt and GOA provenance.
Core interpretation: Chloroplastic radical SAM lipoyl synthase that inserts sulfur atoms into octanoylated lipoyl domains to produce protein-bound lipoate.
Main evidence source: [file:POPTR/LIP1P-2/LIP1P-2-uniprot.txt].

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