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P60716

- LIPA_ECOLI

UniProt

P60716 - LIPA_ECOLI

Protein

Lipoyl synthase

Gene

lipA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 98 (01 Oct 2014)
      Sequence version 1 (13 Apr 2004)
      Previous versions | rss
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    Functioni

    Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. Free octanoate is not a substrate for LipA.3 Publications

    Catalytic activityi

    Protein N(6)-(octanoyl)lysine + 2 sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine = protein N(6)-(lipoyl)lysine + 2 (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine.1 Publication

    Cofactori

    Binds 2 4Fe-4S clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.1 Publication

    Enzyme regulationi

    Inhibited by the AdoMet analog S-adenosyl homocysteine.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi68 – 681Iron-sulfur 1 (4Fe-4S)
    Metal bindingi73 – 731Iron-sulfur 1 (4Fe-4S)
    Metal bindingi79 – 791Iron-sulfur 1 (4Fe-4S)
    Metal bindingi94 – 941Iron-sulfur 2 (4Fe-4S-S-AdoMet)
    Metal bindingi98 – 981Iron-sulfur 2 (4Fe-4S-S-AdoMet)
    Metal bindingi101 – 1011Iron-sulfur 2 (4Fe-4S-S-AdoMet)

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: EcoliWiki
    2. alpha-ketoacid dehydrogenase activity Source: CACAO
    3. lipoate synthase activity Source: EcoliWiki
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. lipoate biosynthetic process Source: EcoliWiki
    2. oxidation-reduction process Source: GOC
    3. protein lipoylation Source: EcoliWiki

    Keywords - Molecular functioni

    Transferase

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11306-MONOMER.
    ECOL316407:JW0623-MONOMER.
    MetaCyc:EG11306-MONOMER.
    UniPathwayiUPA00538; UER00593.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lipoyl synthase (EC:2.8.1.8)
    Alternative name(s):
    Lip-syn
    Short name:
    LS
    Lipoate synthase
    Lipoic acid synthase
    Sulfur insertion protein LipA
    Gene namesi
    Name:lipA
    Synonyms:lip
    Ordered Locus Names:b0628, JW0623
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11306. lipA.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi68 – 7912CEEAS…NLAEC → AEEASAPNLAEA: Loss of 1 4Fe-4S cluster binding. Loss of activity. 1 PublicationAdd
    BLAST
    Mutagenesisi94 – 1018CTRRCPFC → ATRRAPFA: Loss of 1 4Fe-4S cluster binding. Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 321321Lipoyl synthasePRO_0000102313Add
    BLAST

    Proteomic databases

    PaxDbiP60716.
    PRIDEiP60716.

    Expressioni

    Gene expression databases

    GenevestigatoriP60716.

    Interactioni

    Subunit structurei

    Monomer or homodimer.

    Protein-protein interaction databases

    DIPiDIP-48008N.
    IntActiP60716. 13 interactions.
    MINTiMINT-1310776.
    STRINGi511145.b0628.

    Structurei

    3D structure databases

    ProteinModelPortaliP60716.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0320.
    HOGENOMiHOG000235997.
    KOiK03644.
    OMAiHPHIPTK.
    OrthoDBiEOG6038ZS.
    PhylomeDBiP60716.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00206. Lipoyl_synth.
    InterProiIPR013785. Aldolase_TIM.
    IPR006638. Elp3/MiaB/NifB.
    IPR003698. Lipoyl_synth.
    IPR007197. rSAM.
    [Graphical view]
    PANTHERiPTHR10949. PTHR10949. 1 hit.
    PfamiPF04055. Radical_SAM. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005963. Lipoyl_synth. 1 hit.
    SMARTiSM00729. Elp3. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00510. lipA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P60716-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKPIVMERG VKYRDADKMA LIPVKNVATE REALLRKPEW MKIKLPADST    50
    RIQGIKAAMR KNGLHSVCEE ASCPNLAECF NHGTATFMIL GAICTRRCPF 100
    CDVAHGRPVA PDANEPVKLA QTIADMALRY VVITSVDRDD LRDGGAQHFA 150
    DCITAIREKS PQIKIETLVP DFRGRMDRAL DILTATPPDV FNHNLENVPR 200
    IYRQVRPGAD YNWSLKLLER FKEAHPEIPT KSGLMVGLGE TNEEIIEVMR 250
    DLRRHGVTML TLGQYLQPSR HHLPVQRYVS PDEFDEMKAE ALAMGFTHAA 300
    CGPFVRSSYH ADLQAKGMEV K 321
    Length:321
    Mass (Da):36,072
    Last modified:April 13, 2004 - v1
    Checksum:iBE7BF32A4E3AA358
    GO

    Sequence cautioni

    The sequence AAA24072.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti35 – 351L → V(PubMed:1577793)Curated
    Sequence conflicti35 – 351L → V(PubMed:8444795)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M82805 Genomic DNA. Translation: AAA24072.1. Different initiation.
    L07636 Genomic DNA. Translation: AAA66345.1.
    U82598 Genomic DNA. Translation: AAB40828.1.
    U00096 Genomic DNA. Translation: AAC73729.1.
    AP009048 Genomic DNA. Translation: BAA35271.1.
    PIRiB64797.
    RefSeqiNP_415161.1. NC_000913.3.
    YP_488919.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73729; AAC73729; b0628.
    BAA35271; BAA35271; BAA35271.
    GeneIDi12931644.
    945227.
    KEGGiecj:Y75_p0618.
    eco:b0628.
    PATRICi32116437. VBIEscCol129921_0658.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M82805 Genomic DNA. Translation: AAA24072.1 . Different initiation.
    L07636 Genomic DNA. Translation: AAA66345.1 .
    U82598 Genomic DNA. Translation: AAB40828.1 .
    U00096 Genomic DNA. Translation: AAC73729.1 .
    AP009048 Genomic DNA. Translation: BAA35271.1 .
    PIRi B64797.
    RefSeqi NP_415161.1. NC_000913.3.
    YP_488919.1. NC_007779.1.

    3D structure databases

    ProteinModelPortali P60716.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48008N.
    IntActi P60716. 13 interactions.
    MINTi MINT-1310776.
    STRINGi 511145.b0628.

    Proteomic databases

    PaxDbi P60716.
    PRIDEi P60716.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73729 ; AAC73729 ; b0628 .
    BAA35271 ; BAA35271 ; BAA35271 .
    GeneIDi 12931644.
    945227.
    KEGGi ecj:Y75_p0618.
    eco:b0628.
    PATRICi 32116437. VBIEscCol129921_0658.

    Organism-specific databases

    EchoBASEi EB1283.
    EcoGenei EG11306. lipA.

    Phylogenomic databases

    eggNOGi COG0320.
    HOGENOMi HOG000235997.
    KOi K03644.
    OMAi HPHIPTK.
    OrthoDBi EOG6038ZS.
    PhylomeDBi P60716.

    Enzyme and pathway databases

    UniPathwayi UPA00538 ; UER00593 .
    BioCyci EcoCyc:EG11306-MONOMER.
    ECOL316407:JW0623-MONOMER.
    MetaCyc:EG11306-MONOMER.

    Miscellaneous databases

    PROi P60716.

    Gene expression databases

    Genevestigatori P60716.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_00206. Lipoyl_synth.
    InterProi IPR013785. Aldolase_TIM.
    IPR006638. Elp3/MiaB/NifB.
    IPR003698. Lipoyl_synth.
    IPR007197. rSAM.
    [Graphical view ]
    PANTHERi PTHR10949. PTHR10949. 1 hit.
    Pfami PF04055. Radical_SAM. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF005963. Lipoyl_synth. 1 hit.
    SMARTi SM00729. Elp3. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00510. lipA. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The biosynthesis of lipoic acid. Cloning of lip, a lipoate biosynthetic locus of Escherichia coli."
      Hayden M.A., Huang I., Bussiere D.E., Ashley G.W.
      J. Biol. Chem. 267:9512-9515(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Lipoic acid metabolism in Escherichia coli: sequencing and functional characterization of the lipA and lipB genes."
      Reed K.E., Cronan J.E. Jr.
      J. Bacteriol. 175:1325-1336(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. "Escherichia coli LipA is a lipoyl synthase: in vitro biosynthesis of lipoylated pyruvate dehydrogenase complex from octanoyl-acyl carrier protein."
      Miller J.R., Busby R.W., Jordan S.W., Cheek J., Henshaw T.F., Ashley G.W., Broderick J.B., Cronan J.E. Jr., Marletta M.A.
      Biochemistry 39:15166-15178(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, EPR SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
      Strain: BL21-DE3.
    8. "Assembly of the covalent linkage between lipoic acid and its cognate enzymes."
      Zhao X., Miller J.R., Jiang Y., Marletta M.A., Cronan J.E. Jr.
      Chem. Biol. 10:1293-1302(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
      Strain: K12 / JK1.
    9. "Lipoyl synthase requires two equivalents of S-adenosyl-L-methionine to synthesize one equivalent of lipoic acid."
      Cicchillo R.M., Iwig D.F., Jones A.D., Nesbitt N.M., Baleanu-Gogonea C., Souder M.G., Tu L., Booker S.J.
      Biochemistry 43:6378-6386(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    10. "Escherichia coli lipoyl synthase binds two distinct [4Fe-4S] clusters per polypeptide."
      Cicchillo R.M., Lee K.-H., Baleanu-Gogonea C., Nesbitt N.M., Krebs C., Booker S.J.
      Biochemistry 43:11770-11781(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, CHARACTERIZATION, MOESSBAUER SPECTROSCOPY, EPR SPECTROSCOPY, MUTAGENESIS OF 68-CYS--CYS-79 AND 94-CYS--CYS-101.
    11. "Unraveling the pathway of lipoic acid biosynthesis."
      Booker S.J.
      Chem. Biol. 11:10-12(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: PATHWAY.
    12. "Mechanistic investigations of lipoic acid biosynthesis in Escherichia coli: both sulfur atoms in lipoic acid are contributed by the same lipoyl synthase polypeptide."
      Cicchillo R.M., Booker S.J.
      J. Am. Chem. Soc. 127:2860-2861(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: REACTION MECHANISM.

    Entry informationi

    Entry nameiLIPA_ECOLI
    AccessioniPrimary (citable) accession number: P60716
    Secondary accession number(s): P25845, P77595
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 13, 2004
    Last sequence update: April 13, 2004
    Last modified: October 1, 2014
    This is version 98 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The source of sulfurs is the LipA protein itself, most likely one 4Fe-4S cluster.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3