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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: ?

Regulation summary diagram for lipB

Summary:
LipB is a lipoyl-/octanoyl-ACP:protein transferase that catalyzes the first step of de novo lipoate biosynthesis [Jordan97a, Jordan03]. In vitro, it transfers lipoyl or octanoyl domains from the corresponding acylated ACP to its target proteins; in vivo, octanoyl-ACP is the relevant substrate. Lipoate modification of the E2 subunits is important for the function of pyruvate dehydrogenase [Herbert75, Stepp81, Reed93], α-ketoglutarate dehydrogenase [Herbert75, Stepp81, Reed93], and the glycine cleavage system [Vanden91, Reed93].

The LipB protein is translated from a TTG translation initiation codon [Vaisvila00]; protein translated from the downstream ATG is not active [Jordan03]. The LipB-catalyzed reaction proceeds via an acyl-enzyme intermediate. The octanoate group is first transferred from the thiol of ACP to the C169 thiol of LipB, followed by transfer to a specific lysine residue of E2 subunits [Zhao05a]. Substrate recognition appears to include a structural component, as a biotinyl domain (structurally similar to a lipoyl domain) is lipoylated if mutated to contain a lipoylation site of sequence DKA [Reche98]. Structural similarity between lipoylating and biotinylating enzymes, and implications with respect to the catalytic site, are discussed [Reche00].

LipA and LipB interact directly and independently with the E2 protein of both pyruvate dehydrogenase and α-ketoglutarate dehydrogenase, but not GcvH of the glycine cleavage system [Hassan11].

A lipB null mutant exhibits decreased lipoate biosynthesis, decreased pyruvate dehydrogenase activity, and decreased alpha-ketoglutarate dehydrogenase activity compared to wild type. Growth of a lipB mutant can be supported by 6-thiooctanoate or 8-thiooctanoate in place of lipoate [Reed93]. A lipB mutant also exhibits increased transcription from the major promoter of the dam methyltransferase gene, compared to wild type [Vaisvila00]. A heat-sensitive enzyme has been generated [Jordan03]. Duplication of the lipB locus results in resistance to selenolipoic acid [Jordan02]. Genetic interactions have been observed between LplA and the LipB-LipA 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]. Missense mutations in lplA that reduce the enzyme's Km for octanoate can scavenge cytosolic octanoate and thereby suppress the auxotrophic phenotype of a lipB mutant [Hermes09].

LipB appears to be expressed at very low levels; overexpression from a plasmid decreases the growth rate of the cell [Vaisvila00].

Review: [Cronan05]

Citations: [Creaghan78, Chang91a, Miller00a, Hermes14]

Gene Citations: [Nonaka06]

Locations: cytosol

Map Position: [660,860 <- 661,501] (14.24 centisomes, 51°)
Length: 642 bp / 213 aa

Molecular Weight of Polypeptide: 23.883 kD (from nucleotide sequence), 24 kD (experimental) [Vaisvila00 ], 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 , Prosite:IN-FAMILY:PS51733

Gene-Reaction Schematic: ?

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:0009249 - protein lipoylation Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0003824 - catalytic activity Inferred from experiment [Nesbitt05]
GO:0005515 - protein binding Inferred from experiment [Hassan11]
GO:0016415 - octanoyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01a, Jordan97a]
GO:0016740 - transferase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, Jordan03]
GO:0017118 - lipoyltransferase activity Inferred from experiment [Nesbitt05]
GO:0033819 - lipoyl(octanoyl) transferase activity Inferred from experiment Inferred by computational analysis [GOA01, Nesbitt05]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers lipoate

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]

Credits:
Last-Curated ? 06-Nov-2014 by Keseler I , SRI International


Enzymatic reaction of: octanoyl transferase (lipoyl(octanoyl) transferase)

Synonyms: lipoyl(octanoyl) transferase, octanoyl-acyl carrier protein:protein N-octanoyltransferase

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 direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for a [lipoyl-carrier protein]-L-lysine: [glycine cleavage system lipoyl-carrier protein]-L-lysine [Nesbitt05 ] , AceF [Zhao05a ] , SucB [Zhao05a ]

In Pathways: lipoate biosynthesis and incorporation I

Kinetic Parameters:

Substrate
Km (μM)
Citations
[glycine cleavage system lipoyl-carrier protein]-L-lysine
13.2
[Nesbitt05]
an octanoyl-[acp]
10.2
[Nesbitt05]

pH(opt): 7.5 [Nesbitt05]


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.

Kinetic Parameters:

Substrate
Km (μM)
Citations
lipoyl-ACP
1.0
[Jordan03]


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.


Sequence Features

Protein sequence of lipoyl(octanoyl) transferase with features indicated

Feature Class Location Citations Comment
Conserved-Region 32 -> 207
[UniProt14]
UniProt: BPL/LPL catalytic.
Sequence-Conflict 33
[Reed93, UniProt10a]
UniProt: (in Ref. 1; AAA66342);
Protein-Segment 71 -> 78
[UniProt12b]
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
[UniProt15]
UniProt: No effect on activity.
Protein-Segment 138 -> 140
[UniProt12b]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 147
[UniProt15]
UniProt: No effect on activity.
Protein-Segment 151 -> 153
[UniProt12b]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Active-Site 169
[UniProt15]
UniProt: Acyl-thioester intermediate.
Mutagenesis-Variant 169
[Zhao05a, UniProt11a]
[Zhao05a, UniProt11a]
C → A: 1% of wild-type activity.
C → S: Loss of activity.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

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

Chang91a: 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

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

Cronan05: Cronan JE, Zhao X, Jiang Y (2005). "Function, attachment and synthesis of lipoic acid in Escherichia coli." Adv Microb Physiol 50;103-46. PMID: 16221579

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

Hassan11: Hassan BH, Cronan JE (2011). "Protein-protein interactions in assembly of lipoic acid on the 2-oxoacid dehydrogenases of aerobic metabolism." J Biol Chem 286(10);8263-76. PMID: 21209092

Herbert75: Herbert AA, Guest JR (1975). "Lipoic acid content of Escherichia coli and other microorganisms." Arch Microbiol 106(3);259-66. PMID: 814874

Hermes09: Hermes FA, Cronan JE (2009). "Scavenging of cytosolic octanoic acid by mutant LplA lipoate ligases allows growth of Escherichia coli strains lacking the LipB octanoyltransferase of lipoic acid synthesis." J Bacteriol 191(22);6796-803. PMID: 19684135

Hermes14: Hermes FA, Cronan JE (2014). "An NAD Synthetic Reaction Bypasses the Lipoate Requirement for Aerobic Growth of Escherichia coli Strains Blocked in Succinate Catabolism." Mol Microbiol. PMID: 25303731

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

Jordan97a: Jordan SW, Cronan JE (1997). "A new metabolic link. The acyl carrier protein of lipid synthesis donates lipoic acid to the pyruvate dehydrogenase complex in Escherichia coli and mitochondria." J Biol Chem 272(29);17903-6. PMID: 9218413

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

Stepp81: Stepp LR, Bleile DM, McRorie DK, Pettit FH, Reed LJ (1981). "Use of trypsin and lipoamidase to study the role of lipoic acid moieties in the pyruvate and alpha-ketoglutarate dehydrogenase complexes of Escherichia coli." Biochemistry 20(16);4555-60. PMID: 6794598

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.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-14 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms 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

Zhao05a: 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
Page generated by SRI International Pathway Tools version 19.0 on Sun Apr 26, 2015, BIOCYC13A.