P60716 (LIPA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	lipA
Synonyms:	lip
Ordered Locus Names:	b0628, JW0623

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	321 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.7 Ref.8 Ref.9
Catalytic activity	Protein N(6)-(octanoyl)lysine + 2 sulfur + 2 S-adenosyl-L-methionine = protein N(6)-(lipoyl)lysine + 2 L-methionine + 2 5'-deoxyadenosine. Ref.9
Cofactor	Binds 2 4Fe-4S clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Ref.10
Enzyme regulation	Inhibited by the AdoMet analog S-adenosyl homocysteine. HAMAP-Rule MF_00206
Pathway	Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Ref.11
Subunit structure	Monomer or homodimer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00206.
Miscellaneous	The source of sulfurs is the LipA protein itself, most likely one 4Fe-4S cluster. HAMAP-Rule MF_00206
Sequence similarities	Belongs to the radical SAM superfamily. Lipoyl synthase family.
Sequence caution	The sequence AAA24072.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine
Molecular function	Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein lipoylation Inferred from direct assay Ref.9. Source: EcoliWiki
Cellular_component	cytoplasm Inferred from direct assay Ref.9. Source: EcoliWiki
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from direct assay PubMed 10747808. Source: EcoliWiki lipoate synthase activity Inferred from direct assay Ref.9. Source: EcoliWiki metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 321	321	Lipoyl synthase HAMAP-Rule MF_00206		PRO_0000102313
Sites
	Metal binding	68	1	Iron-sulfur 1 (4Fe-4S)
	Metal binding	73	1	Iron-sulfur 1 (4Fe-4S)
	Metal binding	79	1	Iron-sulfur 1 (4Fe-4S)
	Metal binding	94	1	Iron-sulfur 2 (4Fe-4S-S-AdoMet)
	Metal binding	98	1	Iron-sulfur 2 (4Fe-4S-S-AdoMet)
	Metal binding	101	1	Iron-sulfur 2 (4Fe-4S-S-AdoMet)
Experimental info
	Mutagenesis	68 – 79	12	CEEAS…NLAEC → AEEASAPNLAEA: Loss of 1 4Fe-4S cluster binding. Loss of activity. Ref.10
	Mutagenesis	94 – 101	8	CTRRCPFC → ATRRAPFA: Loss of 1 4Fe-4S cluster binding. Loss of activity. Ref.10
	Sequence conflict	35	1	L → V Ref.1
	Sequence conflict	35	1	L → V Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P60716 [UniParc]. Last modified April 13, 2004. Version 1. Checksum: BE7BF32A4E3AA358	FASTA	321	36,072
	10 20 30 40 50 60 MSKPIVMERG VKYRDADKMA LIPVKNVATE REALLRKPEW MKIKLPADST RIQGIKAAMR 70 80 90 100 110 120 KNGLHSVCEE ASCPNLAECF NHGTATFMIL GAICTRRCPF CDVAHGRPVA PDANEPVKLA 130 140 150 160 170 180 QTIADMALRY VVITSVDRDD LRDGGAQHFA DCITAIREKS PQIKIETLVP DFRGRMDRAL 190 200 210 220 230 240 DILTATPPDV FNHNLENVPR IYRQVRPGAD YNWSLKLLER FKEAHPEIPT KSGLMVGLGE 250 260 270 280 290 300 TNEEIIEVMR DLRRHGVTML TLGQYLQPSR HHLPVQRYVS PDEFDEMKAE ALAMGFTHAA 310 320 CGPFVRSSYH ADLQAKGMEV K

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] 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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
PIR	B64797.
RefSeq	NP_415161.1. NC_000913.2. YP_488919.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P60716.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-48008N.
IntAct	P60716. 12 interactions.
MINT	MINT-1310776.
STRING	511145.b0628.
Proteomic databases
PaxDb	P60716.
PRIDE	P60716.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC73729; AAC73729; b0628. BAA35271; BAA35271; BAA35271.
GeneID	12931644. 945227.
KEGG	ecj:Y75_p0618. eco:b0628.
PATRIC	32116437. VBIEscCol129921_0658.
Organism-specific databases
EchoBASE	EB1283.
EcoGene	EG11306. lipA.
Phylogenomic databases
eggNOG	COG0320.
HOGENOM	HOG000235997.
KO	K03644.
OMA	EEYVTPE.
ProtClustDB	PRK05481.
Enzyme and pathway databases
BioCyc	EcoCyc:EG11306-MONOMER. ECOL316407:JW0623-MONOMER. MetaCyc:EG11306-MONOMER.
UniPathway	UPA00538; UER00593.
Gene expression databases
Genevestigator	P60716.
Family and domain databases
Gene3D	3.20.20.70. 1 hit.
HAMAP	MF_00206. Lipoyl_synth.
InterPro	IPR013785. Aldolase_TIM. IPR006638. Elp3/MiaB/NifB. IPR003698. Lipoyl_synth. IPR007197. rSAM. [Graphical view]
PANTHER	PTHR10949. PTHR10949. 1 hit.
Pfam	PF04055. Radical_SAM. 1 hit. [Graphical view]
PIRSF	PIRSF005963. Lipoyl_synth. 1 hit.
SMART	SM00729. Elp3. 1 hit. [Graphical view]
TIGRFAMs	TIGR00510. lipA. 1 hit.
ProtoNet	Search...

Entry information

Entry name

LIPA_ECOLI

Accession

Primary (citable) accession number: P60716
Secondary accession number(s): P25845, P77595

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 13, 2004
Last sequence update:	April 13, 2004
Last modified:	May 1, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program