LIPA_ECOLI
ID LIPA_ECOLI Reviewed; 321 AA.
AC P60716; P25845; P77595;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 13-APR-2004, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Lipoyl synthase {ECO:0000255|HAMAP-Rule:MF_00206};
DE EC=2.8.1.8 {ECO:0000255|HAMAP-Rule:MF_00206, ECO:0000269|PubMed:15157071};
DE AltName: Full=Lip-syn {ECO:0000255|HAMAP-Rule:MF_00206};
DE Short=LS {ECO:0000255|HAMAP-Rule:MF_00206};
DE AltName: Full=Lipoate synthase {ECO:0000255|HAMAP-Rule:MF_00206};
DE AltName: Full=Lipoic acid synthase {ECO:0000255|HAMAP-Rule:MF_00206};
DE AltName: Full=Sulfur insertion protein LipA {ECO:0000255|HAMAP-Rule:MF_00206};
GN Name=lipA {ECO:0000255|HAMAP-Rule:MF_00206}; Synonyms=lip;
GN OrderedLocusNames=b0628, JW0623;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1577793; DOI=10.1016/s0021-9258(19)50120-x;
RA Hayden M.A., Huang I., Bussiere D.E., Ashley G.W.;
RT "The biosynthesis of lipoic acid. Cloning of lip, a lipoate biosynthetic
RT locus of Escherichia coli.";
RL J. Biol. Chem. 267:9512-9515(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8444795; DOI=10.1128/jb.175.5.1325-1336.1993;
RA Reed K.E., Cronan J.E. Jr.;
RT "Lipoic acid metabolism in Escherichia coli: sequencing and functional
RT characterization of the lipA and lipB genes.";
RL J. Bacteriol. 175:1325-1336(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [7]
RP FUNCTION, AND EPR SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
RC STRAIN=BL21-DE3;
RX PubMed=11106496; DOI=10.1021/bi002060n;
RA Miller J.R., Busby R.W., Jordan S.W., Cheek J., Henshaw T.F., Ashley G.W.,
RA Broderick J.B., Cronan J.E. Jr., Marletta M.A.;
RT "Escherichia coli LipA is a lipoyl synthase: in vitro biosynthesis of
RT lipoylated pyruvate dehydrogenase complex from octanoyl-acyl carrier
RT protein.";
RL Biochemistry 39:15166-15178(2000).
RN [8]
RP FUNCTION.
RC STRAIN=K12 / JK1;
RX PubMed=14700636; DOI=10.1016/j.chembiol.2003.11.016;
RA Zhao X., Miller J.R., Jiang Y., Marletta M.A., Cronan J.E. Jr.;
RT "Assembly of the covalent linkage between lipoic acid and its cognate
RT enzymes.";
RL Chem. Biol. 10:1293-1302(2003).
RN [9]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=15157071; DOI=10.1021/bi049528x;
RA Cicchillo R.M., Iwig D.F., Jones A.D., Nesbitt N.M., Baleanu-Gogonea C.,
RA Souder M.G., Tu L., Booker S.J.;
RT "Lipoyl synthase requires two equivalents of S-adenosyl-L-methionine to
RT synthesize one equivalent of lipoic acid.";
RL Biochemistry 43:6378-6386(2004).
RN [10]
RP COFACTOR, CHARACTERIZATION, MOESSBAUER SPECTROSCOPY, EPR SPECTROSCOPY, AND
RP MUTAGENESIS OF 68-CYS--CYS-79 AND 94-CYS--CYS-101.
RX PubMed=15362861; DOI=10.1021/bi0488505;
RA Cicchillo R.M., Lee K.-H., Baleanu-Gogonea C., Nesbitt N.M., Krebs C.,
RA Booker S.J.;
RT "Escherichia coli lipoyl synthase binds two distinct [4Fe-4S] clusters per
RT polypeptide.";
RL Biochemistry 43:11770-11781(2004).
RN [11]
RP PATHWAY.
RX PubMed=15112987; DOI=10.1016/j.chembiol.2004.01.002;
RA Booker S.J.;
RT "Unraveling the pathway of lipoic acid biosynthesis.";
RL Chem. Biol. 11:10-12(2004).
RN [12]
RP ACTIVITY REGULATION.
RX PubMed=15911379; DOI=10.1016/j.chembiol.2005.04.012;
RA Choi-Rhee E., Cronan J.E.;
RT "A nucleosidase required for in vivo function of the S-adenosyl-L-
RT methionine radical enzyme, biotin synthase.";
RL Chem. Biol. 12:589-593(2005).
RN [13]
RP REACTION MECHANISM.
RX PubMed=15740115; DOI=10.1021/ja042428u;
RA Cicchillo R.M., Booker S.J.;
RT "Mechanistic investigations of lipoic acid biosynthesis in Escherichia
RT coli: both sulfur atoms in lipoic acid are contributed by the same lipoyl
RT synthase polypeptide.";
RL J. Am. Chem. Soc. 127:2860-2861(2005).
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. Free octanoate is not
CC a substrate for LipA. {ECO:0000269|PubMed:11106496,
CC ECO:0000269|PubMed:14700636, ECO:0000269|PubMed:15157071}.
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 = (R)-
CC N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S]
CC cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-
CC methionine + 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_00206,
CC ECO:0000269|PubMed:15157071};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00206,
CC ECO:0000269|PubMed:15362861};
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_00206, ECO:0000269|PubMed:15362861};
CC -!- ACTIVITY REGULATION: Is physiologically inhibited by accumulation of
CC the reaction product 5'-deoxyadenosine (PubMed:15911379). Inhibited by
CC the AdoMet analog S-adenosyl homocysteine.
CC {ECO:0000269|PubMed:15911379}.
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_00206,
CC ECO:0000269|PubMed:15112987}.
CC -!- SUBUNIT: Monomer or homodimer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00206}.
CC -!- MISCELLANEOUS: The source of sulfurs is the LipA protein itself, most
CC likely one 4Fe-4S cluster.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. Lipoyl synthase
CC family. {ECO:0000255|HAMAP-Rule:MF_00206, ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA24072.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; M82805; AAA24072.1; ALT_INIT; Genomic_DNA.
DR EMBL; L07636; AAA66345.1; -; Genomic_DNA.
DR EMBL; U82598; AAB40828.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73729.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35271.1; -; Genomic_DNA.
DR PIR; B64797; B64797.
DR RefSeq; NP_415161.1; NC_000913.3.
DR RefSeq; WP_000042632.1; NZ_STEB01000031.1.
DR AlphaFoldDB; P60716; -.
DR SMR; P60716; -.
DR BioGRID; 4260638; 67.
DR BioGRID; 849612; 2.
DR DIP; DIP-48008N; -.
DR IntAct; P60716; 13.
DR STRING; 511145.b0628; -.
DR jPOST; P60716; -.
DR PaxDb; P60716; -.
DR PRIDE; P60716; -.
DR EnsemblBacteria; AAC73729; AAC73729; b0628.
DR EnsemblBacteria; BAA35271; BAA35271; BAA35271.
DR GeneID; 66671098; -.
DR GeneID; 945227; -.
DR KEGG; ecj:JW0623; -.
DR KEGG; eco:b0628; -.
DR PATRIC; fig|1411691.4.peg.1640; -.
DR EchoBASE; EB1283; -.
DR eggNOG; COG0320; Bacteria.
DR HOGENOM; CLU_033144_2_1_6; -.
DR InParanoid; P60716; -.
DR OMA; PYCDIDF; -.
DR PhylomeDB; P60716; -.
DR BioCyc; EcoCyc:EG11306-MON; -.
DR BioCyc; MetaCyc:EG11306-MON; -.
DR BRENDA; 2.8.1.8; 2026.
DR UniPathway; UPA00538; UER00593.
DR PRO; PR:P60716; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoliWiki.
DR GO; GO:0016992; F:lipoate synthase activity; IDA:EcoliWiki.
DR GO; GO:0102552; F:lipoyl synthase activity (acting on glycine-cleavage complex H protein; IEA:UniProtKB-EC.
DR GO; GO:0102553; F:lipoyl synthase activity (acting on pyruvate dehydrogenase E2 protein); IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009107; P:lipoate biosynthetic process; IMP:EcoliWiki.
DR GO; GO:0009249; P:protein lipoylation; IDA:EcoliWiki.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00206; Lipoyl_synth; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR031691; LIAS_N.
DR InterPro; IPR003698; Lipoyl_synth.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR10949; PTHR10949; 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 SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR00510; lipA; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Metal-binding; Reference proteome;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..321
FT /note="Lipoyl synthase"
FT /id="PRO_0000102313"
FT DOMAIN 80..297
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 68
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00206"
FT BINDING 73
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00206"
FT BINDING 79
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00206"
FT BINDING 94
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_00206"
FT BINDING 98
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_00206"
FT BINDING 101
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_00206"
FT BINDING 308
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00206"
FT MUTAGEN 68..79
FT /note="CEEASCPNLAEC->AEEASAPNLAEA: Loss of 1 4Fe-4S cluster
FT binding. Loss of activity."
FT /evidence="ECO:0000269|PubMed:15362861"
FT MUTAGEN 94..101
FT /note="CTRRCPFC->ATRRAPFA: Loss of 1 4Fe-4S cluster
FT binding. Loss of activity."
FT /evidence="ECO:0000269|PubMed:15362861"
FT CONFLICT 35
FT /note="L -> V (in Ref. 1 and 2)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 321 AA; 36072 MW; BE7BF32A4E3AA358 CRC64;
MSKPIVMERG VKYRDADKMA LIPVKNVATE REALLRKPEW MKIKLPADST RIQGIKAAMR
KNGLHSVCEE ASCPNLAECF NHGTATFMIL GAICTRRCPF CDVAHGRPVA PDANEPVKLA
QTIADMALRY VVITSVDRDD LRDGGAQHFA DCITAIREKS PQIKIETLVP DFRGRMDRAL
DILTATPPDV FNHNLENVPR IYRQVRPGAD YNWSLKLLER FKEAHPEIPT KSGLMVGLGE
TNEEIIEVMR DLRRHGVTML TLGQYLQPSR HHLPVQRYVS PDEFDEMKAE ALAMGFTHAA
CGPFVRSSYH ADLQAKGMEV K
