ID LISC_ARATH Reviewed; 394 AA.
AC Q8LEE8; Q8LSZ8; Q9FT94;
DT 05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT 05-OCT-2010, sequence version 2.
DT 24-JAN-2024, entry version 125.
DE RecName: Full=Lipoyl synthase, chloroplastic {ECO:0000255|HAMAP-Rule:MF_03129};
DE EC=2.8.1.8 {ECO:0000255|HAMAP-Rule:MF_03129, ECO:0000269|PubMed:12062419};
DE AltName: Full=Lipoate synthase {ECO:0000255|HAMAP-Rule:MF_03129};
DE Short=LS {ECO:0000255|HAMAP-Rule:MF_03129};
DE Short=Lip-syn {ECO:0000255|HAMAP-Rule:MF_03129};
DE AltName: Full=Lipoate synthase, plastidial {ECO:0000255|HAMAP-Rule:MF_03129};
DE Short=LIP1p {ECO:0000255|HAMAP-Rule:MF_03129};
DE AltName: Full=Lipoic acid synthase {ECO:0000255|HAMAP-Rule:MF_03129};
DE Flags: Precursor;
GN Name=LIP1P {ECO:0000255|HAMAP-Rule:MF_03129};
GN OrderedLocusNames=At5g08415 {ECO:0000312|Araport:AT5G08415};
GN ORFNames=F8L15.140 {ECO:0000312|EMBL:CAC08341.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, TISSUE
RP SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=12062419; DOI=10.1016/s0014-5793(02)02589-9;
RA Yasuno R., Wada H.;
RT "The biosynthetic pathway for lipoic acid is present in plastids and
RT mitochondria in Arabidopsis thaliana.";
RL FEBS Lett. 517:110-114(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Shinn P., Chen H., Kim C.J., Quinitio C., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=23581459; DOI=10.1111/plb.12028;
RA Ewald R., Hoffmann C., Neuhaus E., Bauwe H.;
RT "Two redundant octanoyltransferases and one obligatory lipoyl synthase
RT provide protein-lipoylation autonomy to plastids of Arabidopsis.";
RL Plant Biol. 16:35-42(2014).
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 (PubMed:12062419) (By
CC similarity). Together with LIP2P and LIP2P2 is essential for de novo
CC plastidial protein lipoylation during seed development
CC (PubMed:23581459). {ECO:0000255|HAMAP-Rule:MF_03129,
CC ECO:0000269|PubMed:12062419, ECO:0000269|PubMed:23581459}.
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 ECO:0000269|PubMed:12062419};
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, ECO:0000269|PubMed:12062419}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves and flowers.
CC {ECO:0000269|PubMed:12062419}.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality.
CC {ECO:0000269|PubMed:23581459}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. Lipoyl synthase
CC family. {ECO:0000255|HAMAP-Rule:MF_03129}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM62684.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAC08341.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB073745; BAB91180.1; -; mRNA.
DR EMBL; AL392174; CAC08341.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91298.1; -; Genomic_DNA.
DR EMBL; AY085458; AAM62684.1; ALT_INIT; mRNA.
DR EMBL; BT025549; ABF58967.1; -; mRNA.
DR RefSeq; NP_568196.1; NM_120926.3.
DR AlphaFoldDB; Q8LEE8; -.
DR SMR; Q8LEE8; -.
DR STRING; 3702.Q8LEE8; -.
DR PaxDb; 3702-AT5G08415-1; -.
DR ProteomicsDB; 238385; -.
DR EnsemblPlants; AT5G08415.1; AT5G08415.1; AT5G08415.
DR GeneID; 830740; -.
DR Gramene; AT5G08415.1; AT5G08415.1; AT5G08415.
DR KEGG; ath:AT5G08415; -.
DR Araport; AT5G08415; -.
DR TAIR; AT5G08415; LIP1.
DR eggNOG; KOG2672; Eukaryota.
DR HOGENOM; CLU_033144_2_0_1; -.
DR InParanoid; Q8LEE8; -.
DR OMA; RSCAFCQ; -.
DR OrthoDB; 575at2759; -.
DR PhylomeDB; Q8LEE8; -.
DR UniPathway; UPA00538; UER00593.
DR PRO; PR:Q8LEE8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8LEE8; baseline and differential.
DR Genevisible; Q8LEE8; AT.
DR GO; GO:0009507; C:chloroplast; 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 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; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR SUPFAM; SSF102114; Radical SAM enzymes; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Chloroplast; Iron; Iron-sulfur; Metal-binding; Plastid;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; Transit peptide.
FT TRANSIT 1..36
FT /note="Chloroplast"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03129"
FT CHAIN 37..394
FT /note="Lipoyl synthase, chloroplastic"
FT /id="PRO_0000398858"
FT DOMAIN 141..362
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 127
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P9WK91, ECO:0000255|HAMAP-
FT Rule:MF_03129"
FT BINDING 132
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P9WK91, ECO:0000255|HAMAP-
FT Rule:MF_03129"
FT BINDING 138
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P9WK91, ECO:0000255|HAMAP-
FT Rule:MF_03129"
FT BINDING 158
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:0000250|UniProtKB:P9WK91, ECO:0000255|HAMAP-
FT Rule:MF_03129"
FT BINDING 162
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:0000250|UniProtKB:P9WK91, ECO:0000255|HAMAP-
FT Rule:MF_03129"
FT BINDING 165
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:0000250|UniProtKB:P9WK91, ECO:0000255|HAMAP-
FT Rule:MF_03129"
FT BINDING 373
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P9WK91, ECO:0000255|HAMAP-
FT Rule:MF_03129"
SQ SEQUENCE 394 AA; 43622 MW; 3F1B081CF0216255 CRC64;
MMHHCSITKP TFSISISTQK LHHHSSKFLN LGFRIRCESG DVSSPLRTKA VSLSSEMEDS
SSLKKSLMEL EGKKSEPYPG GMPKMGPFTG RDPNVKKPAW LRQKAPQGER FQEVKESLSR
LNLNTVCEEA QCPNIGECWN GGGDGVATAT IMVLGDTCTR GCRFCAVKTS RNPPPPDPME
PENTAKAIAS WGVDYIVITS VDRDDIPDGG SGHFAQTVKA MKRHKPDIMI ECLTSDFRGD
LEAVDTLVHS GLDVFAHNVE TVKRLQRLVR DPRAGYEQSM SVLKHAKISK PGMITKTSIM
LGLGETDEEL KEAMADLRAI DVDILTLGQY LQPTPLHLTV KEYVTPEKFD FWKTYGESIG
FRYVASGPLV RSSYRAGELF VKTMVKESYS KSLS
//
