LIP1P-1

UniProt ID: B9I666
Organism: Populus trichocarpa
Review Status: DRAFT
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Gene Description

Chloroplastic radical SAM lipoyl synthase that inserts sulfur atoms into octanoylated lipoyl domains to produce protein-bound lipoate.

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-1, but GO:0009107 was obsoleted (2026-08-22) in favor of protein lipoylation.
Reason: LIP1P-1 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-1/LIP1P-1-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-1/LIP1P-1-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-1/LIP1P-1-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-1, but GO:0009107 was obsoleted (2026-08-22) in favor of protein lipoylation.
Reason: LIP1P-1 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-1/LIP1P-1-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-1/LIP1P-1-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-1/LIP1P-1-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-1/LIP1P-1-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-1/LIP1P-1-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-1/LIP1P-1-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-1/LIP1P-1-uniprot.txt
COFACTOR: Binds 2 [4Fe-4S] clusters per subunit.
GO:1904047 S-adenosyl-L-methionine binding
IC
file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt 		NEW
Summary: LIP1P-1 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-1 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-1/LIP1P-1-uniprot.txt
Note=Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated
file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
cysteines and an exchangeable S-adenosyl-L-methionine
file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
/ligand_note="4Fe-4S-S-AdoMet"

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-1/LIP1P-1-uniprot.txt
    FUNCTION: Catalyzes the radical-mediated insertion of two sulfur atoms into the octanoyl moiety bound to lipoyl domains.
  • file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
    CATALYTIC ACTIVITY: EC=2.8.1.8.
  • file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
    SUBCELLULAR LOCATION: Plastid, chloroplast.

Binds the catalytic radical SAM [4Fe-4S] cluster through the CxxxCxxC motif; its unique iron coordinates the S-adenosyl-L-methionine that is reductively cleaved to the 5'-deoxyadenosyl radical starting every turnover of lipoate synthase activity. A second [4Fe-4S] cluster is the sacrificial source of the two sulfur atoms inserted into the octanoyl chain.

Molecular Function:
4 iron, 4 sulfur cluster binding
Supporting Evidence:
  • file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
    Note=Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated
  • file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
    cysteines and an exchangeable S-adenosyl-L-methionine

Binds S-adenosyl-L-methionine as the radical-generating cosubstrate at the unique iron of the [4Fe-4S] cluster: two SAM are consumed per lipoyl group formed.

Molecular Function:
S-adenosyl-L-methionine binding
Supporting Evidence:
  • file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
    cysteines and an exchangeable S-adenosyl-L-methionine
  • file:POPTR/LIP1P-1/LIP1P-1-uniprot.txt
    /ligand_note="4Fe-4S-S-AdoMet"

References

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Suggested Questions for Experts

Q: Do LIP1P-1 and LIP1P-2 have redundant or tissue-specific roles in chloroplast protein lipoylation?

Suggested Experiments

Experiment: Compare lipoylated chloroplast enzyme abundance in isoform-specific knockdown lines.

Type: targeted functional assay

📚 Additional Documentation

Notes

(LIP1P-1-notes.md)

LIP1P-1 notes

  • Reviewed existing GOA annotations against LIP1P-1-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-1/LIP1P-1-uniprot.txt].

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