ID   LISC2_POPTR             Reviewed;         397 AA.
AC   B9N2B0; U5FF64;
DT   05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT   24-MAR-2009, sequence version 1.
DT   27-MAR-2024, entry version 90.
DE   RecName: Full=Lipoyl synthase 2, chloroplastic;
DE            EC=2.8.1.8 {ECO:0000255|HAMAP-Rule:MF_03129};
DE   AltName: Full=Lipoate synthase 2 {ECO:0000255|HAMAP-Rule:MF_03129};
DE            Short=LS 2 {ECO:0000255|HAMAP-Rule:MF_03129};
DE            Short=Lip-syn 2 {ECO:0000255|HAMAP-Rule:MF_03129};
DE   AltName: Full=Lipoate synthase, plastidial 2 {ECO:0000255|HAMAP-Rule:MF_03129};
DE            Short=LIP1p 2 {ECO:0000255|HAMAP-Rule:MF_03129};
DE   AltName: Full=Lipoic acid synthase 2 {ECO:0000255|HAMAP-Rule:MF_03129};
DE   Flags: Precursor;
GN   Name=LIP1P-2 {ECO:0000255|HAMAP-Rule:MF_03129};
GN   ORFNames=POPTR_0019s13380g;
OS   Populus trichocarpa (Western balsam poplar) (Populus balsamifera subsp.
OS   trichocarpa).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus.
OX   NCBI_TaxID=3694;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nisqually;
RX   PubMed=16973872; DOI=10.1126/science.1128691;
RA   Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I.,
RA   Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J.,
RA   Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W.,
RA   Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M.,
RA   Chapman J., Chen G.-L., Cooper D., Coutinho P.M., Couturier J., Covert S.,
RA   Cronk Q., Cunningham R., Davis J., Degroeve S., Dejardin A.,
RA   dePamphilis C.W., Detter J., Dirks B., Dubchak I., Duplessis S.,
RA   Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J.,
RA   Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y.,
RA   Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S.,
RA   Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjaervi J., Karlsson J.,
RA   Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F.,
RA   Leebens-Mack J., Leple J.-C., Locascio P., Lou Y., Lucas S., Martin F.,
RA   Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O.,
RA   Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J.,
RA   Richardson P., Rinaldi C., Ritland K., Rouze P., Ryaboy D., Schmutz J.,
RA   Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A.,
RA   Tsai C.-J., Uberbacher E., Unneberg P., Vahala J., Wall K., Wessler S.,
RA   Yang G., Yin T., Douglas C., Marra M., Sandberg G., Van de Peer Y.,
RA   Rokhsar D.S.;
RT   "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).";
RL   Science 313:1596-1604(2006).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nisqually;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Grigoriev I.V., Terry A., Salamov A.A., Otillar R., Lou Y., Lucas S.,
RA   Hammon N., Glavina del Rio T., Detter J., Kalin E., Tice H., Pitluck S.,
RA   Chapman J., Putnam N.H., Brunner A., Busov V., Campbell M., Chalot M.,
RA   Covert S., Davis J., DiFazio S., Gribskov M., Gunter L., Hamberger B.,
RA   Jansson S., Joshi C., Larimer F., Martin F., Napoli C., Nelson D.,
RA   Ralph S., Rombauts S., Rouze P., Schrader J., Tsai C., Vahala J.,
RA   Tuskan G., Rokhsar D.;
RL   Submitted (DEC-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_03129}.
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_03129};
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_03129};
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_03129};
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_03129}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255|HAMAP-
CC       Rule:MF_03129}.
CC   -!- SIMILARITY: Belongs to the radical SAM superfamily. Lipoyl synthase
CC       family. {ECO:0000255|HAMAP-Rule:MF_03129}.
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DR   EMBL; CM009308; ERP49380.1; -; Genomic_DNA.
DR   RefSeq; XP_006371583.1; XM_006371521.1.
DR   AlphaFoldDB; B9N2B0; -.
DR   SMR; B9N2B0; -.
DR   STRING; 3694.B9N2B0; -.
DR   EnsemblPlants; Potri.019G102700.1.v4.1; Potri.019G102700.1.v4.1; Potri.019G102700.v4.1.
DR   GeneID; 18108579; -.
DR   Gramene; Potri.019G102700.1.v4.1; Potri.019G102700.1.v4.1; Potri.019G102700.v4.1.
DR   KEGG; pop:18108579; -.
DR   eggNOG; KOG2672; Eukaryota.
DR   HOGENOM; CLU_033144_2_0_1; -.
DR   InParanoid; B9N2B0; -.
DR   OMA; FAYWKEY; -.
DR   OrthoDB; 575at2759; -.
DR   UniPathway; UPA00538; UER00593.
DR   Proteomes; UP000006729; Chromosome 19.
DR   ExpressionAtlas; B9N2B0; baseline and differential.
DR   GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR   GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016992; F:lipoate synthase activity; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0009107; P:lipoate biosynthetic process; IBA:GO_Central.
DR   CDD; cd01335; Radical_SAM; 1.
DR   Gene3D; 3.20.20.70; Aldolase class I; 1.
DR   HAMAP; MF_00206; Lipoyl_synth; 1.
DR   HAMAP; MF_03129; Lipoyl_synth_plantC; 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; IPR027526; Lipoyl_synth_chlpt.
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   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; Chloroplast; Iron; Iron-sulfur; Metal-binding; Plastid;
KW   Reference proteome; S-adenosyl-L-methionine; Transferase; Transit peptide.
FT   TRANSIT         1..35
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03129"
FT   CHAIN           36..397
FT                   /note="Lipoyl synthase 2, chloroplastic"
FT                   /id="PRO_0000398868"
FT   DOMAIN          142..363
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   REGION          49..85
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        49..71
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
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_03129"
FT   BINDING         133
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03129"
FT   BINDING         139
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03129"
FT   BINDING         159
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_03129"
FT   BINDING         163
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_03129"
FT   BINDING         166
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_03129"
FT   BINDING         374
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03129"
SQ   SEQUENCE   397 AA;  43638 MW;  FC77A8FC05480DA9 CRC64;
     MIEQSLSKPS FSLSIPIPKA PKSKSSFFCS YSKIRCESVD YPSLTKIDAK HPQNSTTINN
     GSSSSASVDL KNNEKGPYPY PGGGKMGPYT GRDLNEKKPE WLRQRAPQGE RFEEVKESIS
     RLNLNTVCQE AQCPNIGECW NGGGDGIATA TIMVLGDTCT RGCRFCAVKT SRTPPPPDPM
     EPLNTALAIA SWGVDYIVIT SVDRDDLSDG GSGHFAQTVR AMKELKPEIM VECLTSDFRG
     DLKAVDTLVH SGLDVFAHNV ETVKRLQRIV RDPRAGYEQS LSVLKHAKVS KKGMITKTSI
     MLGLGETDDE VKEAMTDLRA IDVDILTFGQ YLQPTPLHLT VKEYVSPEKF AYWKEYGESI
     GFRYVASGPL VRSSYRAGEL FVKTMVKESA KEAAAIS
//