ID   LIPA2_PHATC             Reviewed;         314 AA.
AC   B7G3Y9;
DT   05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT   10-FEB-2009, sequence version 1.
DT   24-JAN-2024, entry version 71.
DE   RecName: Full=Lipoyl synthase 2, mitochondrial;
DE            EC=2.8.1.8 {ECO:0000255|HAMAP-Rule:MF_03123};
DE   AltName: Full=Lipoate synthase 2 {ECO:0000255|HAMAP-Rule:MF_03123};
DE            Short=LS 2 {ECO:0000255|HAMAP-Rule:MF_03123};
DE            Short=Lip-syn 2 {ECO:0000255|HAMAP-Rule:MF_03123};
DE   AltName: Full=Lipoic acid synthase 2 {ECO:0000255|HAMAP-Rule:MF_03123};
GN   ORFNames=PHATRDRAFT_28652;
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   -!- MISCELLANEOUS: This protein may be expected to contain an N-terminal
CC       transit peptide but none has been predicted. {ECO:0000255|HAMAP-
CC       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; CM000615; EEC46905.1; -; Genomic_DNA.
DR   RefSeq; XP_002181691.1; XM_002181655.1.
DR   AlphaFoldDB; B7G3Y9; -.
DR   SMR; B7G3Y9; -.
DR   STRING; 556484.B7G3Y9; -.
DR   PaxDb; 2850-Phatr28652; -.
DR   GeneID; 7202486; -.
DR   KEGG; pti:PHATRDRAFT_28652; -.
DR   eggNOG; KOG2672; Eukaryota.
DR   HOGENOM; CLU_033144_2_0_1; -.
DR   InParanoid; B7G3Y9; -.
DR   OrthoDB; 575at2759; -.
DR   UniPathway; UPA00538; UER00593.
DR   Proteomes; UP000000759; Chromosome 13.
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; 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; PF04055; Radical_SAM; 1.
DR   PIRSF; PIRSF005963; Lipoyl_synth; 1.
DR   SFLD; SFLDF00271; lipoyl_synthase; 1.
DR   SFLD; SFLDS00029; Radical_SAM; 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.
FT   CHAIN           1..314
FT                   /note="Lipoyl synthase 2, mitochondrial"
FT                   /id="PRO_0000398244"
FT   DOMAIN          58..276
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   REGION          1..21
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         46
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         51
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         57
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         72
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         76
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         79
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         287
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   314 AA;  34862 MW;  70E379E29A535340 CRC64;
     MPKGRPSWFK VPAPSQGTQS TYSTASYSRY AQVKDSLQKL DLHTVCEEAQ CPNIGECWNG
     GTGTIMLLGD TCTRGCMFCA VNTDSKPPPP DPFEPFKTAE AVVAWGVDYI VLTSVDRDDI
     ADGGAQHFAQ TVQLLKQNKP NLLVECLVSD FQGMLDSVET LALSGLDVYA HNVETVERLQ
     PFVRDARANY QQSLSTLQHA KVVKPELYTK TSIMLGLGET EEEVTQTMTD LRAIGVDVVT
     FGQYLRPTEH HLSVVEYVTP EKFDHYRQVG ENMGFKYVAS GPMVRSSYKA GEFYLEHMIK
     KERTEAAIDI GENA
//