ID   LIPA1_PHATC             Reviewed;         401 AA.
AC   B7FRU7;
DT   05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT   10-FEB-2009, sequence version 1.
DT   24-JAN-2024, entry version 70.
DE   RecName: Full=Lipoyl synthase 1, mitochondrial;
DE            EC=2.8.1.8 {ECO:0000255|HAMAP-Rule:MF_03123};
DE   AltName: Full=Lipoate synthase 1 {ECO:0000255|HAMAP-Rule:MF_03123};
DE            Short=LS 1 {ECO:0000255|HAMAP-Rule:MF_03123};
DE            Short=Lip-syn 1 {ECO:0000255|HAMAP-Rule:MF_03123};
DE   AltName: Full=Lipoic acid synthase 1 {ECO:0000255|HAMAP-Rule:MF_03123};
DE   Flags: Precursor;
GN   ORFNames=PHATRDRAFT_18029;
OS   Phaeodactylum tricornutum (strain CCAP 1055/1).
OC   Eukaryota; Sar; Stramenopiles; Ochrophyta; Bacillariophyta;
OC   Bacillariophyceae; Bacillariophycidae; Naviculales; Phaeodactylaceae;
OC   Phaeodactylum.
OX   NCBI_TaxID=556484;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CCAP 1055/1;
RX   PubMed=18923393; DOI=10.1038/nature07410;
RA   Bowler C., Allen A.E., Badger J.H., Grimwood J., Jabbari K., Kuo A.,
RA   Maheswari U., Martens C., Maumus F., Otillar R.P., Rayko E., Salamov A.,
RA   Vandepoele K., Beszteri B., Gruber A., Heijde M., Katinka M., Mock T.,
RA   Valentin K., Verret F., Berges J.A., Brownlee C., Cadoret J.P.,
RA   Chiovitti A., Choi C.J., Coesel S., De Martino A., Detter J.C., Durkin C.,
RA   Falciatore A., Fournet J., Haruta M., Huysman M.J., Jenkins B.D.,
RA   Jiroutova K., Jorgensen R.E., Joubert Y., Kaplan A., Kroger N., Kroth P.G.,
RA   La Roche J., Lindquist E., Lommer M., Martin-Jezequel V., Lopez P.J.,
RA   Lucas S., Mangogna M., McGinnis K., Medlin L.K., Montsant A.,
RA   Oudot-Le Secq M.P., Napoli C., Obornik M., Parker M.S., Petit J.L.,
RA   Porcel B.M., Poulsen N., Robison M., Rychlewski L., Rynearson T.A.,
RA   Schmutz J., Shapiro H., Siaut M., Stanley M., Sussman M.R., Taylor A.R.,
RA   Vardi A., von Dassow P., Vyverman W., Willis A., Wyrwicz L.S.,
RA   Rokhsar D.S., Weissenbach J., Armbrust E.V., Green B.R., Van de Peer Y.,
RA   Grigoriev I.V.;
RT   "The Phaeodactylum genome reveals the evolutionary history of diatom
RT   genomes.";
RL   Nature 456:239-244(2008).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=CCAP 1055/1;
RG   Diatom Consortium;
RA   Grigoriev I., Grimwood J., Kuo A., Otillar R.P., Salamov A., Detter J.C.,
RA   Lindquist E., Shapiro H., Lucas S., Glavina del Rio T., Pitluck S.,
RA   Rokhsar D., Bowler C.;
RL   Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Catalyzes the radical-mediated insertion of two sulfur atoms
CC       into the C-6 and C-8 positions of the octanoyl moiety bound to the
CC       lipoyl domains of lipoate-dependent enzymes, thereby converting the
CC       octanoylated domains into lipoylated derivatives. {ECO:0000255|HAMAP-
CC       Rule:MF_03123}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=[[Fe-S] cluster scaffold protein carrying a second [4Fe-
CC         4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2
CC         oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-
CC         deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2
CC         hydrogen sulfide + 2 L-methionine + N(6)-[(R)-dihydrolipoyl]-L-lysyl-
CC         [protein] + 2 reduced [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:16585,
CC         Rhea:RHEA-COMP:9928, Rhea:RHEA-COMP:10000, Rhea:RHEA-COMP:10001,
CC         Rhea:RHEA-COMP:10475, Rhea:RHEA-COMP:14568, Rhea:RHEA-COMP:14569,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:17319, ChEBI:CHEBI:29034,
CC         ChEBI:CHEBI:29919, ChEBI:CHEBI:33722, ChEBI:CHEBI:33737,
CC         ChEBI:CHEBI:33738, ChEBI:CHEBI:57844, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:78809, ChEBI:CHEBI:83100; EC=2.8.1.8;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_03123};
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_03123};
CC       Note=Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated
CC       with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
CC       {ECO:0000255|HAMAP-Rule:MF_03123};
CC   -!- PATHWAY: Protein modification; protein lipoylation via endogenous
CC       pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-
CC       protein]: step 2/2. {ECO:0000255|HAMAP-Rule:MF_03123}.
CC   -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03123}.
CC   -!- SIMILARITY: Belongs to the radical SAM superfamily. Lipoyl synthase
CC       family. {ECO:0000255|HAMAP-Rule:MF_03123}.
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DR   EMBL; CM000606; EEC50372.1; -; Genomic_DNA.
DR   RefSeq; XP_002177558.1; XM_002177522.1.
DR   AlphaFoldDB; B7FRU7; -.
DR   SMR; B7FRU7; -.
DR   STRING; 556484.B7FRU7; -.
DR   PaxDb; 2850-Phatr18029; -.
DR   EnsemblProtists; Phatr3_J18029.t1; Phatr3_J18029.p1; Phatr3_J18029.
DR   GeneID; 7197080; -.
DR   KEGG; pti:PHATRDRAFT_18029; -.
DR   eggNOG; KOG2672; Eukaryota.
DR   HOGENOM; CLU_033144_2_0_1; -.
DR   InParanoid; B7FRU7; -.
DR   OMA; PYCDIDF; -.
DR   OrthoDB; 575at2759; -.
DR   UniPathway; UPA00538; UER00593.
DR   Proteomes; UP000000759; Chromosome 2.
DR   GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016992; F:lipoate synthase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   CDD; cd01335; Radical_SAM; 1.
DR   Gene3D; 3.20.20.70; Aldolase class I; 1.
DR   HAMAP; MF_00206; Lipoyl_synth; 1.
DR   InterPro; IPR013785; Aldolase_TIM.
DR   InterPro; IPR006638; Elp3/MiaA/NifB-like_rSAM.
DR   InterPro; IPR031691; LIAS_N.
DR   InterPro; IPR003698; Lipoyl_synth.
DR   InterPro; IPR007197; rSAM.
DR   NCBIfam; TIGR00510; lipA; 1.
DR   PANTHER; PTHR10949; LIPOYL SYNTHASE; 1.
DR   PANTHER; PTHR10949:SF0; LIPOYL SYNTHASE, MITOCHONDRIAL; 1.
DR   Pfam; PF16881; LIAS_N; 1.
DR   Pfam; PF04055; Radical_SAM; 1.
DR   PIRSF; PIRSF005963; Lipoyl_synth; 1.
DR   SFLD; SFLDF00271; lipoyl_synthase; 1.
DR   SFLD; SFLDG01058; lipoyl_synthase_like; 1.
DR   SMART; SM00729; Elp3; 1.
DR   SUPFAM; SSF102114; Radical SAM enzymes; 1.
DR   PROSITE; PS51918; RADICAL_SAM; 1.
PE   3: Inferred from homology;
KW   4Fe-4S; Iron; Iron-sulfur; Metal-binding; Mitochondrion;
KW   Reference proteome; S-adenosyl-L-methionine; Transferase; Transit peptide.
FT   TRANSIT         1..25
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
FT   CHAIN           26..401
FT                   /note="Lipoyl synthase 1, mitochondrial"
FT                   /id="PRO_0000398243"
FT   DOMAIN          133..365
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   REGION          49..79
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        49..74
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         117
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
FT   BINDING         122
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
FT   BINDING         128
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
FT   BINDING         148
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="2"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
FT   BINDING         152
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="2"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
FT   BINDING         155
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="2"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
FT   BINDING         376
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03123"
SQ   SEQUENCE   401 AA;  44192 MW;  C5270EA0E1E231A9 CRC64;
     MWSSSSSLCR NPSFRRAWLS TVTVTQTAAP TSSRLAALRT QLATEEASID DFSSTNAPTT
     TTHYTSSNGS PIVRQKAAPR SAKILPKPRW LKAAPATSDN YRKLRDTVRE LGLATVCEEA
     RCPNIGECWG GGEDQTATAT IMIMGDTCTR GCRFCSVKTS RAPPPLDPHE PEKVATAIAQ
     WGLDYVVLTS VDRDDLPDQG ADHFRQVVTQ LKLKKPSLLV EALTPDFQGN MDLVHAVATS
     GLDVYAHNME TVEALTPKVR DRRATYRQSL EVLRYVKTIQ SDPIGTTNNH NNNNGCLTKT
     SLMLGLGETD DQVLTTLRDL RDADVDVVTF GQYLQPTKKH LPVQEYVTPE KFDFWQETAM
     GMGFAYVASG PLVRSSYKAG ELFLQKYIAQ KKQRNAEVAA A
//