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Escherichia coli K-12 substr. MG1655 Enzyme: lipoyl(octanoyl) transferase



Gene: lipB Accession Numbers: EG11591 (EcoCyc), b0630, ECK0623

Synonyms: cde, lip, lipoyl-[acyl-carrier-protein]-protein-N-lipoyltransferase, lipoyl (octanoyl)-acyl carrier protein:protein transferase, lipoate-protein ligase B, lipoyl-protein ligase

Regulation Summary Diagram: ?

Summary:
LipB is a lipoyl-protein ligase that specifically utilizes LipA-generated lipoyl-ACP, in contrast to the other lipoyl-protein ligase, LplA, which utilizes lipoate imported from outside the cell [Morris95]. LipB-mediated transfer of lipoic or octanoic acid moiety from the corresponding acylated ACP derivative to pyruvate dehydrogenase (AceE) lipoyl domain has been observed in vitro [Jordan03]. Substrate recognition appears to include a structural component, as a biotinyl domein (structurally similar to a lipoyl domain) is lipoylated if mutated to contain a lipoylation site of sequence DKA [Reche98].

A lipB null mutant exhibits decreased lipoic acid biosynthesis, decreased pyruvate dehydrogenase activity, and decreased alpha-ketoglutarate dehydrogenase activity compared to wild type [Reed93]. A lipB mutant also exhibits increased transcription from the major promoter of the dam methylase gene, compared to wild type [Vaisvila00]. A heat-sensitive enzyme has been generated [Jordan03]. Duplication of the lip loci results in resistance to selenolipoic acid [Jordan02]. LipA and LipB are necessary for anaerobic glycine cleavage system activity [Reed93]. The lipoic acid auxotrophy of a lipB mutant is rescued by 6-thiooctanoic acid or 8-thiooctanoic acid [Reed93]. Genetic interactions have been observed between LplA and the LipA to LipB pathway; phenotypes of an lipB mutant are suppressed by overproduction of LplA, and lplA lipA or lplA lipB double mutants exhibit growth defects, whereas an lplA single mutant does not [Morris95].

The protein is translated from a TTG codon [Vaisvila00] and protein translated from the downstream ATG is not active [Jordan03].

LipB has 27% identity to Kluyveromyces lactis LIPB lipoyl-protein ligase [Chen97] and has similarity to Arabidopsis thaliana LIP2 protein [Wada01]. Structural similarity between lipoylating and biotinylating enzymes, and implications with respect to the catalytic site, are discussed [Reche00]. Phenotypes of a lipB mutant are functionally complemented by Arabidopsis thaliana LIP2 protein [Wada01].

An in vitro assay is described for activity of LipA with LplA or with LipB [Miller00a]. An in vitro assay with purified LipB is described [Jordan03].

Regulation has been described. Abundance of LipB is lower at stationary phase than during log phase growth [Vaisvila00].

Citations: [Vanden91, Creaghan78, Chang91]

Gene Citations: [Nonaka06]

Locations: cytosol

Map Position: [660,860 <- 661,501] (14.24 centisomes)
Length: 642 bp / 213 aa

Molecular Weight of Polypeptide: 23.883 kD (from nucleotide sequence), 24 kD (experimental), 25 kD (experimental)

Unification Links: ASAP:ABE-0002160 , CGSC:555 , EchoBASE:EB1549 , EcoGene:EG11591 , EcoliWiki:b0630 , OU-Microarray:b0630 , PortEco:lipB , PR:PRO_000023093 , Pride:P60720 , Protein Model Portal:P60720 , RefSeq:NP_415163 , RegulonDB:EG11591 , SMR:P60720 , String:511145.b0630 , UniProt:P60720

Relationship Links: InterPro:IN-FAMILY:IPR000544 , InterPro:IN-FAMILY:IPR004143 , InterPro:IN-FAMILY:IPR020605 , Panther:IN-FAMILY:PTHR10993:SF0 , Pfam:IN-FAMILY:PF03099 , Prosite:IN-FAMILY:PS01313

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006464 - cellular protein modification process Inferred from experiment Inferred by computational analysis [GOA01a, Nesbitt05]
GO:0009106 - lipoate metabolic process Inferred from experiment [Vanden91]
GO:0009107 - lipoate biosynthetic process Inferred from experiment Inferred by computational analysis [GOA01a, Reed93]
GO:0010629 - negative regulation of gene expression Inferred from experiment [Vaisvila00]
GO:0009059 - macromolecule biosynthetic process
Molecular Function: GO:0003824 - catalytic activity Inferred from experiment [Nesbitt05]
GO:0016740 - transferase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Jordan03]
GO:0017118 - lipoyltransferase activity Inferred from experiment [Nesbitt05]
GO:0016415 - octanoyltransferase activity Inferred by computational analysis [GOA01a]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0033819 - lipoyl(octanoyl) transferase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents)

Essentiality data for lipB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Enzymatic reaction of: lipoyl-protein ligase (lipoyl(octanoyl) transferase)

[glycine cleavage system lipoyl-carrier protein]-L-lysine + a lipoyl-[acp] <=> a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + a holo-[acyl-carrier protein] + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.


Enzymatic reaction of: lipoyl-protein ligase (lipoyl(octanoyl) transferase)

SucB + lipoyl-ACP <=> SucB-lipoate + a holo-[acyl-carrier protein]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.


Enzymatic reaction of: lipoyl-protein ligase (lipoyl(octanoyl) transferase)

AceF + lipoyl-ACP <=> AceF-lipoate + a holo-[acyl-carrier protein]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.


Enzymatic reaction of: lipoyl(octanoyl) transferase

Synonyms: lipoyl-protein ligase

EC Number: 2.3.1.181

an octanoyl-[acp] + a [lipoyl-carrier protein]-L-lysine <=> a [lipoyl-carrier protein] N6-octanoyl-L-lysine + a holo-[acyl-carrier protein] + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: lipoate biosynthesis and incorporation I


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 33
[Reed93, UniProt10a]
Alternate sequence: S → D; UniProt: (in Ref. 1; AAA66342);
Protein-Segment 71 -> 78
[UniProt12a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 135
[UniProt10]
UniProt: Lowers pKa of active site Cys; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 137
[UniProt10a]
Alternate sequence: C → A; UniProt: No effect on activity;
Protein-Segment 138 -> 140
[UniProt12a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 147
[UniProt10a]
Alternate sequence: C → A; UniProt: No effect on activity;
Protein-Segment 151 -> 153
[UniProt12a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 169
[Zhao05, UniProt11]
Alternate sequence: C → S; UniProt: Loss of activity.
Alternate sequence: C → A; UniProt: 1% of wild-type activity.
Active-Site 169
[UniProt10a]
UniProt: Acyl-thioester intermediate;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b0630 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11591; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Chang91: Chang YY, Cronan JE, Li SJ, Reed K, Vanden Boom T, Wang AY (1991). "Locations of the lip, poxB, and ilvBN genes on the physical map of Escherichia coli." J Bacteriol 173(17);5258-9. PMID: 1832150

Chen97: Chen XJ (1997). "Cloning and characterization of the lipoyl-protein ligase gene LIPB from the yeast Kluyveromyces lactis: synergistic respiratory deficiency due to mutations in LIPB and mitochondrial F1-ATPase subunits." Mol Gen Genet 255(3);341-9. PMID: 9268025

Creaghan78: Creaghan IT, Guest JR (1978). "Succinate dehydrogenase-dependent nutritional requirement for succinate in mutants of Escherichia coli K12." J Gen Microbiol 107(1);1-13. PMID: 366070

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Jordan02: Jordan SW, Cronan JE (2002). "Chromosomal amplification of the Escherichia coli lipB region confers high-level resistance to selenolipoic acid." J Bacteriol 184(19);5495-501. PMID: 12218038

Jordan03: Jordan SW, Cronan JE (2003). "The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase." J Bacteriol 185(5);1582-9. PMID: 12591875

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Miller00a: Miller JR, Busby RW, Jordan SW, Cheek J, Henshaw TF, Ashley GW, Broderick JB, Cronan JE, Marletta MA (2000). "Escherichia coli LipA is a lipoyl synthase: in vitro biosynthesis of lipoylated pyruvate dehydrogenase complex from octanoyl-acyl carrier protein." Biochemistry 39(49);15166-78. PMID: 11106496

Morris95: Morris TW, Reed KE, Cronan JE (1995). "Lipoic acid metabolism in Escherichia coli: the lplA and lipB genes define redundant pathways for ligation of lipoyl groups to apoprotein." J Bacteriol 177(1);1-10. PMID: 8002607

Nesbitt05: Nesbitt NM, Baleanu-Gogonea C, Cicchillo RM, Goodson K, Iwig DF, Broadwater JA, Haas JA, Fox BG, Booker SJ (2005). "Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase." Protein Expr Purif 39(2);269-82. PMID: 15642479

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Reche00: Reche PA (2000). "Lipoylating and biotinylating enzymes contain a homologous catalytic module." Protein Sci 9(10);1922-9. PMID: 11106165

Reche98: Reche P, Li YL, Fuller C, Eichhorn K, Perham RN (1998). "Selectivity of post-translational modification in biotinylated proteins: the carboxy carrier protein of the acetyl-CoA carboxylase of Escherichia coli." Biochem J 329 ( Pt 3);589-96. PMID: 9445386

Reed93: Reed KE, Cronan JE (1993). "Lipoic acid metabolism in Escherichia coli: sequencing and functional characterization of the lipA and lipB genes." J Bacteriol 175(5);1325-36. PMID: 8444795

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vaisvila00: Vaisvila R, Rasmussen LJ, Lobner-Olesen A, von Freiesleben U, Marinus MG (2000). "The LipB protein is a negative regulator of dam gene expression in Escherichia coli." Biochim Biophys Acta 1494(1-2);43-53. PMID: 11072067

Vanden91: Vanden Boom TJ, Reed KE, Cronan JE (1991). "Lipoic acid metabolism in Escherichia coli: isolation of null mutants defective in lipoic acid biosynthesis, molecular cloning and characterization of the E. coli lip locus, and identification of the lipoylated protein of the glycine cleavage system." J Bacteriol 173(20);6411-20. PMID: 1655709

Wada01: Wada M, Yasuno R, Jordan SW, Cronan JE, Wada H (2001). "Lipoic acid metabolism in Arabidopsis thaliana: cloning and characterization of a cDNA encoding lipoyltransferase." Plant Cell Physiol 42(6);650-6. PMID: 11427685

Zhao05: Zhao X, Miller JR, Cronan JE (2005). "The reaction of LipB, the octanoyl-[acyl carrier protein]:protein N-octanoyltransferase of lipoic acid synthesis, proceeds through an acyl-enzyme intermediate." Biochemistry 44(50);16737-46. PMID: 16342964

Other References Related to Gene Regulation

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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