ID R5VD04_9BACT Unreviewed; 286 AA.
AC R5VD04;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 27-MAR-2024, entry version 49.
DE RecName: Full=Lipoyl synthase {ECO:0000256|HAMAP-Rule:MF_00206};
DE EC=2.8.1.8 {ECO:0000256|HAMAP-Rule:MF_00206};
DE AltName: Full=Lip-syn {ECO:0000256|HAMAP-Rule:MF_00206};
DE Short=LS {ECO:0000256|HAMAP-Rule:MF_00206};
DE AltName: Full=Lipoate synthase {ECO:0000256|HAMAP-Rule:MF_00206};
DE AltName: Full=Lipoic acid synthase {ECO:0000256|HAMAP-Rule:MF_00206};
DE AltName: Full=Sulfur insertion protein LipA {ECO:0000256|HAMAP-Rule:MF_00206};
GN Name=lipA {ECO:0000256|HAMAP-Rule:MF_00206};
GN ORFNames=BN709_00771 {ECO:0000313|EMBL:CCZ81416.1};
OS Odoribacter laneus CAG:561.
OC Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Odoribacteraceae;
OC Odoribacter.
OX NCBI_TaxID=1263089 {ECO:0000313|EMBL:CCZ81416.1, ECO:0000313|Proteomes:UP000017974};
RN [1] {ECO:0000313|EMBL:CCZ81416.1, ECO:0000313|Proteomes:UP000017974}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MGS:561 {ECO:0000313|Proteomes:UP000017974};
RA Nielsen H.B., Almeida M., Juncker A.S., Rasmussen S., Li J., Sunagawa S.,
RA Plichta D., Gautier L., Le Chatelier E., Peletier E., Bonde I., Nielsen T.,
RA Manichanh C., Arumugam M., Batto J., Santos M.B.Q.D., Blom N., Borruel N.,
RA Burgdorf K.S., Boumezbeur F., Casellas F., Dore J., Guarner F., Hansen T.,
RA Hildebrand F., Kaas R.S., Kennedy S., Kristiansen K., Kultima J.R.,
RA Leonard P., Levenez F., Lund O., Moumen B., Le Paslier D., Pons N.,
RA Pedersen O., Prifti E., Qin J., Raes J., Tap J., Tims S., Ussery D.W.,
RA Yamada T., MetaHit consortium, Renault P., Sicheritz-Ponten T., Bork P.,
RA Wang J., Brunak S., Ehrlich S.D.;
RT "Dependencies among metagenomic species, viruses, plasmids and units of
RT genetic variation.";
RL Submitted (NOV-2012) 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:0000256|HAMAP-
CC Rule:MF_00206}.
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:0000256|ARBA:ARBA00043709, ECO:0000256|HAMAP-
CC Rule:MF_00206};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00206};
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:0000256|HAMAP-Rule:MF_00206};
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:0000256|HAMAP-Rule:MF_00206}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00206}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. Lipoyl synthase
CC family. {ECO:0000256|HAMAP-Rule:MF_00206}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:CCZ81416.1}.
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DR EMBL; CBAQ010000070; CCZ81416.1; -; Genomic_DNA.
DR AlphaFoldDB; R5VD04; -.
DR UniPathway; UPA00538; UER00593.
DR Proteomes; UP000017974; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; 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; 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 {ECO:0000256|HAMAP-Rule:MF_00206};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00206};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_00206};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_00206};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00206}; Reference proteome {ECO:0000313|Proteomes:UP000017974};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW Rule:MF_00206}; Transferase {ECO:0000256|HAMAP-Rule:MF_00206}.
FT DOMAIN 50..264
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT BINDING 38
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00206"
FT BINDING 43
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00206"
FT BINDING 49
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00206"
FT BINDING 64
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:0000256|HAMAP-Rule:MF_00206"
FT BINDING 68
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:0000256|HAMAP-Rule:MF_00206"
FT BINDING 71
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:0000256|HAMAP-Rule:MF_00206"
FT BINDING 275
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00206"
SQ SEQUENCE 286 AA; 31754 MW; 9B3DB6D234924A31 CRC64;
MGCNSRRKPE WLKIKLPKGQ LSVEVLNIVR EHHLHTICTS GMCPNQGECW GCGTATFMIG
GNICTRNCRF CNVTTGRPLP LDPGEPHHIA SSVKLLHLKH AVITSVDRDD LEDLGATHWV
KVIRAVKEMN PSVTMEVLIP DFQGRSELIG QIIEAKPEVI SHNLETVRRL TKEIRSRATY
DMSLGVVHQV AASGIVAKSG IMLGLGETRE EILETMDDLR AAGCAVMTIG QYLQPTAANV
EVKEYITPET FEEYRHIGMQ KGFTHVESGP LVRSSYHAEK HVKQAE
//
