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P60716

- LIPA_ECOLI

UniProt

P60716 - LIPA_ECOLI

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Protein

Lipoyl synthase

Gene

lipA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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
Complete GO annotation...

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
Complete GO annotation...

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.
InParanoidiP60716.
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

        10         20         30         40         50
MSKPIVMERG VKYRDADKMA LIPVKNVATE REALLRKPEW MKIKLPADST
60 70 80 90 100
RIQGIKAAMR KNGLHSVCEE ASCPNLAECF NHGTATFMIL GAICTRRCPF
110 120 130 140 150
CDVAHGRPVA PDANEPVKLA QTIADMALRY VVITSVDRDD LRDGGAQHFA
160 170 180 190 200
DCITAIREKS PQIKIETLVP DFRGRMDRAL DILTATPPDV FNHNLENVPR
210 220 230 240 250
IYRQVRPGAD YNWSLKLLER FKEAHPEIPT KSGLMVGLGE TNEEIIEVMR
260 270 280 290 300
DLRRHGVTML TLGQYLQPSR HHLPVQRYVS PDEFDEMKAE ALAMGFTHAA
310 320
CGPFVRSSYH ADLQAKGMEV K
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.
InParanoidi P60716.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 99 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