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Escherichia coli K-12 substr. MG1655 Enzyme: AceF



Gene: aceF Accession Numbers: EG10025 (EcoCyc), b0115, ECK0114

Regulation Summary Diagram: ?

Component of: pyruvate dehydrogenase (extended summary available)

Alternative forms of AceF:
AceF-dihydrolipoate
AceF-S-acetyldihydrolipoate
AceF-lipoate

Summary:
AceF, the "E2" or "core" component of the pyruvate dehydrogenase multienzyme complex, assembles into a 24-subunit [Angelides79] cube [Yang85, Wagenknecht90]. The E1 dimers of the pyruvate dehydrogenase multienzyme complex catalyze acetylation of the lipoate moieties that are attached to the E2 subunits [Danson78]. The E2 subunits (AceF) also exhibit transacetylation [Stanley81]. The structure of the pyruvate dehydrogenase multienzyme complex and the spatial distribution of the E2 lipoyl moieties have been studied by scanning transmission electron microscopy [Yang94].

AceF is a soluble cytoplasmic protein [Schulze92] that contains an acidic N-terminal lipoyl domain with three roughly 100-residue repeats, each with a lipoyl modification motif and an alanine- and proline-rich segment [Packman84, Stephens83]. A single lipoyl domain suffices with respect to enzyme activity and protein function [Guest85]. The lipoyl domains appear to function independently of each other [Allen89]. Lipoyl modification sites (of sequence GDKASME, lipoylated on the lysine) of all three lipoyl domain repeats appear to be fully lipoylated, and all of these lipoyl groups are subject to acetylation by the pyruvate dehydrogenase complex [Packman91]. Individual isolated lipoyl domains show differing capacity to bind lipoic acid [Miles87b]. The enzyme shows a preference for R-lipoic acid, but it can utilize the S-lipoic acid enantiomer [Loeffelhardt96]. A K143Q mutant protein (lacking a functional lipoic acid attachment site in the N-terminal repeat) exhibits some defect inactive site coupling and a two-fold decrease in catalytic activity, compared to wild type [Allen89]. Modification of the E2 subunit plays a role in feedback regulation of pyruvate dehydrogenase multienzyme complex activity; reductive acetylation of the E2 lipoyl groups stimulates the kinase activity of the E1 subunit bound to this group, and the kinase activity then inhibits the pyruvate dehydrogenase multienzyme complex [Ravindran96]. Binding to the E1 subunit has been examined; residue D17 of the E1 subunit is essential and E1 residue D24 plays a role in binding [Hengeveld02].

The AceF alanine- and proline-rich region is a flexible linker [Texter88] that plays a role in active site coupling and is important for catalytic activity [Miles88]. Mutations or moderate deletions within the alanine- and proline-rich linker region, in the context of a mutant protein with only one of the three lipoyl domains, do not compromise the function of the enzyme [Miles87a, Texter88, Miles88], whereas deletion to 13 or fewer amino acids causes defects [Miles88].

AceF also contains a C-terminal catalytic and subunit binding domain [Packman86, Packman84, Stephens83]. The enzyme is sensitive to deletions within this C-terminal domain [Guest85]. The residue S550 is important [Russell91a] and the residue H602 is essential [Russell92] for catalysis .

AceF has similar overall domain organization to SucB, the analogous protein in the 2-oxoglutarate dehydrogenase complex; however, the SucB N terminus contains only one lipoyl repeat and the precise location of the alanine- and proline-rich segment differs among the two proteins [Spencer84, Packman87].

The human pyruvate dehydrogenase E2 subunit has epitopes that are recognized by autoantibodies associated with primary biliary cirrhosis [Gershwin00] and antibodies associated with some cases of active pulmonary tuberculosis (mycobacterial infection) [Klein93].

An aceF mutant has reduced ability to act as a recipient in cell-to-cell transfer of a plasmid [Kurono12].

Regulation has been described [Langley78a, Guest80, Stephens83, Spencer85, Haydon93, Quail94, Henaut98, deGraef99, Ravindran96].

Review: [Perham87]

Citations: [Guest83a, Danson81, Hackert83, Langley77, CaJacob85a, Adamson86, Yang86, Harrison90, Nemeria02, Wei03, Akiyama80]

Gene Citations: [Cunningham98b]

Locations: cytosol

Map Position: [125,695 -> 127,587] (2.71 centisomes)
Length: 1893 bp / 630 aa

Molecular Weight of Polypeptide: 66.096 kD (from nucleotide sequence)

pI: 5.26

Unification Links: ASAP:ABE-0000400 , CGSC:26530 , DIP:DIP-9040N , EchoBASE:EB0024 , EcoGene:EG10025 , EcoliWiki:b0115 , Mint:MINT-1311573 , ModBase:P06959 , OU-Microarray:b0115 , PortEco:aceF , PR:PRO_000022039 , Pride:P06959 , Protein Model Portal:P06959 , RegulonDB:EG10025 , SMR:P06959 , String:511145.b0115 , Swiss-Model:P06959 , UniProt:P06959

Relationship Links: InterPro:IN-FAMILY:IPR000089 , InterPro:IN-FAMILY:IPR001078 , InterPro:IN-FAMILY:IPR003016 , InterPro:IN-FAMILY:IPR004167 , InterPro:IN-FAMILY:IPR006256 , InterPro:IN-FAMILY:IPR011053 , InterPro:IN-FAMILY:IPR023213 , PDB:Structure:1QJO , PDB:Structure:2K7V , Pfam:IN-FAMILY:PF00198 , Pfam:IN-FAMILY:PF00364 , Pfam:IN-FAMILY:PF02817 , Prosite:IN-FAMILY:PS00189 , Prosite:IN-FAMILY:PS50968

In Paralogous Gene Group: 39 (2 members)

In Reactions of unknown directionality:

Not in pathways:
ATP + AceF + (R)-lipoate = AMP + AceF-lipoate + diphosphate
AceF + lipoyl-ACP = AceF-lipoate + a holo-[acyl-carrier protein]

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006086 - acetyl-CoA biosynthetic process from pyruvate Inferred from experiment [Langley78a]
GO:0006090 - pyruvate metabolic process Inferred from experiment [Langley78a]
GO:0055114 - oxidation-reduction process Inferred from experiment [Guest85]
GO:0006096 - glycolytic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004742 - dihydrolipoyllysine-residue acetyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Wei03]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06, Lasserre06, Butland05]
GO:0031405 - lipoic acid binding Inferred from experiment [Wei03]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Lasserre06]
GO:0045254 - pyruvate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01a, Langley77, Guest85]
GO:0005829 - cytosol

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism glyoxylate degradation
metabolism energy metabolism, carbon pyruvate dehydrogenase

Essentiality data for aceF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
No [Feist07, Comment 3]

Enzymatic reaction of: lipoate acetyltransferase (AceF)

EC Number: 2.3.1.12

acetyl-CoA + a [pyruvate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine <=> a [pyruvate dehydrogenase E2 protein] N6-S-acetyldihydrolipoyl-L-lysine + coenzyme A

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 favored in the opposite direction.

In Pathways: pyruvate decarboxylation to acetyl CoA


Subunit of: pyruvate dehydrogenase

Subunit composition of pyruvate dehydrogenase = [(AceE)2]12[AceF]24[(Lpd)2]6
         pyruvate dehydrogenase = (AceE)2 (summary available)
                 subunit of E1p component of pyruvate dehydrogenase complex = AceE
         lipoamide dehydrogenase = (Lpd)2 (extended summary available)
                 E3 monomer = Lpd

Summary:
Pyruvate dehydrogenase is one of the most complicated enzyme systems known. The self-assembling complex is composed of multiple copies of three enzymes: E1, E2 and E3, in stoichiometry of 24:24:12, respectively (12 AceE dimers, a 24-subunit AceF core, and 6 LpdA dimers) [Reed75, Bates77, Yang85, CaJacob85, Angelides79].

AceF, the "E2" or "core" component of the pyruvate dehydrogenase multienzyme complex, assembles into a 24-subunit [Angelides79] cube [Yang85, Wagenknecht90]. The E1 dimers of the pyruvate dehydrogenase multienzyme complex catalyze acetylation of the lipoate moieties that are attached to the E2 subunits [Danson78]. The E2 subunits (AceF) also exhibit transacetylation [Stanley81]. The structure of the pyruvate dehydrogenase multienzyme complex and the spatial distribution of the E2 lipoyl moieties have been studied by scanning transmission electron microscopy [Yang94]. Electron cryotomography showed that the E1 and E3 subunits are flexibly tethered to the E2 core [Murphy05].

The E3 component is shared with 2-oxoglutarate dehydrogenase and glycine cleavage multi-enzyme complexes. E1 and E2 differ slightly between 2-oxoglutarate and pyruvate complexes, and are designated (o) and (p) to distinguish them. Substrate is channeled through the catalytic reactions by attachment in thioester linkage to lipoyl groups via so-called 'swinging arm', carrying substrate molecules to successive active sites [Perham87].

The reaction catalyzed by the pyruvate dehydrogenase multienzyme complex is the gateway to the TCA cycle, producing acetylCoA for the first reaction. In animals, the reaction is regulated by phosphorylation of the E1 component, but not in E. coli [Patel90].


Enzymatic reaction of: pyruvate dehydrogenase

Synonyms: pyruvate dehydrogenase complex, pyruvate dehydrogenase, PDH complex

EC Number: 1.2.1.-

pyruvate + coenzyme A + NAD+ <=> acetyl-CoA + CO2 + NADH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: pyruvate decarboxylation to acetyl CoA , superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass

Cofactors or Prosthetic Groups: thiamin diphosphate [Kale07], FAD [Lindsay00], Mg2+ [Kale07]

Inhibitors (Competitive): fluoropyruvate [Saumweber81] , hydroxypyruvate [Bisswanger81] , 2-oxobutanoate [Saumweber81, Bisswanger81] , glyoxylate [Bisswanger81] , 3-bromopyruvate [Bisswanger81]

Inhibitors (Unknown Mechanism): NADH [Sun12] , tellurite [Contreras10] , tetrahydro-TPP [Williams90, Helmward89] , thiamine thiothiazolone pyrophosphate [Williams90, Helmward89] , NAD+ [Graham89, Comment 4] , pyruvate [Helmward89, Williams90]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Link97, UniProt11a]
UniProt: Removed.
Conserved-Region 2 -> 74
[UniProt09]
UniProt: Lipoyl-binding 1;
Chain 2 -> 630
[UniProt09]
UniProt: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex;
N6-lipoyllysine-Modification 41
[UniProt11]
UniProt: N6-lipoyllysine.
Conserved-Region 106 -> 177
[UniProt09]
UniProt: Lipoyl-binding 2;
N6-lipoyllysine-Modification 144
[UniProt11]
UniProt: N6-lipoyllysine.
Conserved-Region 207 -> 278
[UniProt09]
UniProt: Lipoyl-binding 3;
N6-lipoyllysine-Modification 245
[UniProt11]
UniProt: N6-lipoyllysine.
Protein-Segment 317 -> 630
[UniProt10]
UniProt: Subunit binding, catalytic; Sequence Annotation Type: region of interest;
Acetylation-Modification 366
[Yu08]
 
Protein-Segment 373 -> 389
[UniProt10]
UniProt: Hydrophobic; Sequence Annotation Type: region of interest;
Acetylation-Modification 396
[Zhang09a, UniProt10a]
UniProt: N6-acetyllysine;
Protein-Segment 542 -> 567
[UniProt10]
UniProt: Hydrophobic; Sequence Annotation Type: region of interest;
Active-Site 547
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;
Mutagenesis-Variant 603
[Russell90, UniProt11a]
Alternate sequence: H → C; UniProt: Abolishes catalytic activity.
Active-Site 603
[UniProt10a]
Active-Site 607
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0115 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10025; confirmed by SwissProt match.


References

Adamson86: Adamson SR, Holmes CF, Stevenson KJ (1986). "Acetylatable lipoic acid residues interact directly with lipoamide dehydrogenase in the pyruvate dehydrogenase multienzyme complex of Escherichia coli." Biochem Cell Biol 64(3);250-5. PMID: 3087386

Akiyama80: Akiyama SK, Hammes GG (1980). "Elementary steps in the reaction mechanism of the pyruvate dehydrogenase multienzyme complex from Escherichia coli: kinetics of acetylation and deacetylation." Biochemistry 1980;19(18);4208-13. PMID: 6998493

Allen89: Allen AG, Perham RN, Allison N, Miles JS, Guest JR (1989). "Reductive acetylation of tandemly repeated lipoyl domains in the pyruvate dehydrogenase multienzyme complex of Escherichia coli is random order." J Mol Biol 208(4);623-33. PMID: 2509711

Angelides79: Angelides KJ, Akiyama SK, Hammes GG (1979). "Subunit stoichiometry and molecular weight of the pyruvate dehydrogenase multienzyme complex from Escherichia coli." Proc Natl Acad Sci U S A 1979;76(7);3279-83. PMID: 386335

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Bates77: Bates DL, Danson MJ, Hale G, Hooper EA, Perham RN (1977). "Self-assembly and catalytic activity of the pyruvate dehydrogenase multienzyme complex of Escherichia coli." Nature 268(5618);313-6. PMID: 329143

Bisswanger81: Bisswanger H (1981). "Substrate specificity of the pyruvate dehydrogenase complex from Escherichia coli." J Biol Chem 256(2);815-22. PMID: 7005225

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

CaJacob85: CaJacob CA, Frey PA, Hainfeld JF, Wall JS, Yang H (1985). "Escherichia coli pyruvate dehydrogenase complex: particle masses of the complex and component enzymes measured by scanning transmission electron microscopy." Biochemistry 1985;24(10);2425-31. PMID: 3925985

CaJacob85a: CaJacob CA, Gavino GR, Frey PA (1985). "Pyruvate dehydrogenase complex of Escherichia coli. Thiamin pyrophosphate and NADH-dependent hydrolysis of acetyl-CoA." J Biol Chem 260(27);14610-15. PMID: 3902834

Contreras10: Contreras Ndel P, Vasquez CC (2010). "Tellurite-induced carbonylation of the Escherichia coli pyruvate dehydrogenase multienzyme complex." Arch Microbiol 192(11);969-73. PMID: 20821193

Cunningham98b: Cunningham L, Guest JR (1998). "Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli." Microbiology 144 ( Pt 8);2113-23. PMID: 9720032

Danson78: Danson MJ, Hooper EA, Perham RN (1978). "Intramolecular coupling of active sites in the pyruvate dehydrogenase multienzyme complex of Escherichia coli." Biochem J 175(1);193-8. PMID: 367364

Danson81: Danson MJ, Hale G, Perham RN (1981). "The role of lipoic acid residues in the pyruvate dehydrogenase multienzyme complex of Escherichia coli." Biochem J 199(3);505-11. PMID: 6803765

deGraef99: de Graef MR, Alexeeva S, Snoep JL, Teixeira de Mattos MJ (1999). "The steady-state internal redox state (NADH/NAD) reflects the external redox state and is correlated with catabolic adaptation in Escherichia coli." J Bacteriol 181(8);2351-7. PMID: 10197995

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gershwin00: Gershwin ME, Ansari AA, Mackay IR, Nakanuma Y, Nishio A, Rowley MJ, Coppel RL (2000). "Primary biliary cirrhosis: an orchestrated immune response against epithelial cells." Immunol Rev 174;210-25. PMID: 10807518

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."

Graham89: Graham LD, Packman LC, Perham RN (1989). "Kinetics and specificity of reductive acylation of lipoyl domains from 2-oxo acid dehydrogenase multienzyme complexes." Biochemistry 1989;28(4);1574-81. PMID: 2655695

Guest80: Guest JR, Stephens PE (1980). "Molecular cloning of the pyruvate dehydrogenase complex genes of Escherichia coli." J Gen Microbiol 121(Pt. 2);277-92. PMID: 6455499

Guest83a: Guest JR, Roberts RE, Stephens PE (1983). "Hybrid plasmids containing the pyruvate dehydrogenase complex genes and gene-DNA relationships in the 2 to 3 minute region of the Escherichia coli chromosome." J Gen Microbiol 129 (Pt 3);671-80. PMID: 6308128

Guest85: Guest JR, Lewis HM, Graham LD, Packman LC, Perham RN (1985). "Genetic reconstruction and functional analysis of the repeating lipoyl domains in the pyruvate dehydrogenase multienzyme complex of Escherichia coli." J Mol Biol 185(4);743-54. PMID: 3903169

Hackert83: Hackert ML, Oliver RM, Reed LJ (1983). "A computer model analysis of the active-site coupling mechanism in the pyruvate dehydrogenase multienzyme complex of Escherichia coli." Proc Natl Acad Sci U S A 80(10);2907-11. PMID: 6344073

Harrison90: Harrison JP, Morrison IE, Cherry RJ (1990). "Rotational diffusion studies of the lipoyl domain of 2-oxoacid dehydrogenase multienzyme complexes." Biochemistry 29(23);5596-604. PMID: 1696836

Haydon93: Haydon DJ, Quail MA, Guest JR (1993). "A mutation causing constitutive synthesis of the pyruvate dehydrogenase complex in Escherichia coli is located within the pdhR gene." FEBS Lett 336(1);43-7. PMID: 8262214

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

Henaut98: Henaut A, Lisacek F, Nitschke P, Moszer I, Danchin A (1998). "Global analysis of genomic texts: the distribution of AGCT tetranucleotides in the Escherichia coli and Bacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes." Electrophoresis 19(4);515-27. PMID: 9588797

Hengeveld02: Hengeveld AF, de Kok A (2002). "Identification of the E2-binding residues in the N-terminal domain of E1 of a prokaryotic pyruvate dehydrogenase complex." FEBS Lett 522(1-3);173-6. PMID: 12095640

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

Kale07: Kale S, Arjunan P, Furey W, Jordan F (2007). "A dynamic loop at the active center of the Escherichia coli pyruvate dehydrogenase complex E1 component modulates substrate utilization and chemical communication with the E2 component." J Biol Chem 282(38);28106-16. PMID: 17635929

Klein93: Klein R, Wiebel M, Engelhart S, Berg PA (1993). "Sera from patients with tuberculosis recognize the M2a-epitope (E2-subunit of pyruvate dehydrogenase) specific for primary biliary cirrhosis." Clin Exp Immunol 92(2);308-16. PMID: 7683589

Kurono12: Kurono N, Matsuda A, Etchuya R, Sobue R, Sasaki Y, Ito M, Ando T, Maeda S (2012). "Genome-wide screening of Escherichia coli genes involved in execution and promotion of cell-to-cell transfer of non-conjugative plasmids: rodZ (yfgA) is essential for plasmid acceptance in recipient cells." Biochem Biophys Res Commun 421(1);119-23. PMID: 22497891

Langley77: Langley D, Guest JR (1977). "Biochemical genetics of the alpha-keto acid dehydrogenase complexes of Escherichia coli K12: isolation and biochemical properties of deletion mutants." J Gen Microbiol 99(2);263-76. PMID: 327021

Langley78a: Langley D, Guest JR (1978). "Biochemical genetics of the alpha-keto acid dehydrogenase complexes of Escherichia coli K12: genetic characterization and regulatory properties of deletion mutants." J Gen Microbiol 106(1);103-17. PMID: 349114

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Lindsay00: Lindsay H, Beaumont E, Richards SD, Kelly SM, Sanderson SJ, Price NC, Lindsay JG (2000). "FAD insertion is essential for attaining the assembly competence of the dihydrolipoamide dehydrogenase (E3) monomer from Escherichia coli." J Biol Chem 275(47);36665-70. PMID: 10970889

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Loeffelhardt96: Loeffelhardt S, Borbe HO, Locher M, Bisswanger H (1996). "In vivo incorporation of lipoic acid enantiomers and homologues in the pyruvate dehydrogenase complex from Escherichia coli." Biochim Biophys Acta 1297(1);90-8. PMID: 8841385

Miles87a: Miles JS, Guest JR, Radford SE, Perham RN (1987). "A mutant pyruvate dehydrogenase complex of Escherichia coli deleted in the (alanine + proline)-rich region of the acetyltransferase component." Biochim Biophys Acta 913(2);117-21. PMID: 3297160

Miles87b: Miles JS, Guest JR (1987). "Subgenes expressing single lipoyl domains of the pyruvate dehydrogenase complex of Escherichia coli." Biochem J 245(3);869-74. PMID: 3117051

Miles88: Miles JS, Guest JR, Radford SE, Perham RN (1988). "Investigation of the mechanism of active site coupling in the pyruvate dehydrogenase multienzyme complex of Escherichia coli by protein engineering." J Mol Biol 202(1);97-106. PMID: 3050122

Murphy05: Murphy GE, Jensen GJ (2005). "Electron cryotomography of the E. coli pyruvate and 2-oxoglutarate dehydrogenase complexes." Structure 13(12);1765-73. PMID: 16338405

Nemeria02: Nemeria N, Arjunan P, Brunskill A, Sheibani F, Wei W, Yan Y, Zhang S, Jordan F, Furey W (2002). "Histidine 407, a phantom residue in the E1 subunit of the Escherichia coli pyruvate dehydrogenase complex, activates reductive acetylation of lipoamide on the E2 subunit. An explanation for conservation of active sites between the E1 subunit and transketolase." Biochemistry 41(52);15459-67. PMID: 12501174

Packman84: Packman LC, Hale G, Perham RN (1984). "Repeating functional domains in the pyruvate dehydrogenase multienzyme complex of Escherichia coli." EMBO J 1984;3(6);1315-9. PMID: 6430694

Packman86: Packman LC, Perham RN (1986). "Chain folding in the dihydrolipoyl acyltransferase components of the 2-oxo-acid dehydrogenase complexes from Escherichia coli. Identification of a segment involved in binding the E3 subunit." FEBS Lett 206(2);193-8. PMID: 3530810

Packman87: Packman LC, Perham RN (1987). "Limited proteolysis and sequence analysis of the 2-oxo acid dehydrogenase complexes from Escherichia coli. Cleavage sites and domains in the dihydrolipoamide acyltransferase components." Biochem J 242(2);531-8. PMID: 3297046

Packman91: Packman LC, Green B, Perham RN (1991). "Lipoylation of the E2 components of the 2-oxo acid dehydrogenase multienzyme complexes of Escherichia coli." Biochem J 277 ( Pt 1);153-8. PMID: 1854331

Patel90: Patel MS, Roche TE (1990). "Molecular biology and biochemistry of pyruvate dehydrogenase complexes." FASEB J 1990;4(14);3224-33. PMID: 2227213

Perham87: Perham RN, Packman LC, Radford SE (1987). "2-Oxo acid dehydrogenase multi-enzyme complexes: in the beginning and halfway there." Biochem Soc Symp 1987;54;67-81. PMID: 3332999

Quail94: Quail MA, Haydon DJ, Guest JR (1994). "The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex." Mol Microbiol 12(1);95-104. PMID: 8057842

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Ravindran96: Ravindran S, Radke GA, Guest JR, Roche TE (1996). "Lipoyl domain-based mechanism for the integrated feedback control of the pyruvate dehydrogenase complex by enhancement of pyruvate dehydrogenase kinase activity." J Biol Chem 271(2);653-62. PMID: 8557670

Reed75: Reed LJ, Pettit FH, Eley MH, Hamilton L, Collins JH, Oliver RM (1975). "Reconstitution of the Escherichia coli pyruvate dehydrogenase complex." Proc Natl Acad Sci U S A 1975;72(8);3068-72. PMID: 1103138

Russell90: Russell GC, Guest JR (1990). "Overexpression of restructured pyruvate dehydrogenase complexes and site-directed mutagenesis of a potential active-site histidine residue." Biochem J 269(2);443-50. PMID: 2201286

Russell91a: Russell GC, Guest JR (1991). "Site-directed mutagenesis of the lipoate acetyltransferase of Escherichia coli." Proc R Soc Lond B Biol Sci 243(1307);155-60. PMID: 1676519

Russell92: Russell GC, Machado RS, Guest JR (1992). "Overproduction of the pyruvate dehydrogenase multienzyme complex of Escherichia coli and site-directed substitutions in the E1p and E2p subunits." Biochem J 1992;287 ( Pt 2);611-9. PMID: 1445221

Saumweber81: Saumweber H, Binder R, Bisswanger H (1981). "Pyruvate dehydrogenase component of the pyruvate dehydrogenase complex from Escherichia coli K12. Purification and characterization." Eur J Biochem 1981;114(2);407-11. PMID: 7011811

Schulze92: Schulze E, Westphal AH, Veenhuis M, de Kok A (1992). "Purification and cellular localization of wild type and mutated dihydrolipoyltransacetylases from Azotobacter vinelandii and Escherichia coli expressed in E. coli." Biochim Biophys Acta 1120(1);87-96. PMID: 1554745

Spencer84: Spencer ME, Darlison MG, Stephens PE, Duckenfield IK, Guest JR (1984). "Nucleotide sequence of the sucB gene encoding the dihydrolipoamide succinyltransferase of Escherichia coli K12 and homology with the corresponding acetyltransferase." Eur J Biochem 141(2);361-74. PMID: 6376124

Spencer85: Spencer ME, Guest JR (1985). "Transcription analysis of the sucAB, aceEF and lpd genes of Escherichia coli." Mol Gen Genet 1985;200(1);145-54. PMID: 3897791

Stanley81: Stanley CJ, Packman LC, Danson MJ, Henderson CE, Perham RN (1981). "Intramolecular coupling of active sites in the pyruvate dehydrogenase multienzyme complexes from bacterial and mammalian sources." Biochem J 195(3);715-21. PMID: 7032507

Stephens83: Stephens PE, Darlison MG, Lewis HM, Guest JR (1983). "The pyruvate dehydrogenase complex of Escherichia coli K12. Nucleotide sequence encoding the dihydrolipoamide acetyltransferase component." Eur J Biochem 1983;133(3);481-9. PMID: 6345153

Sun12: Sun Z, Do PM, Rhee MS, Govindasamy L, Wang Q, Ingram LO, Shanmugam KT (2012). "Amino acid substitutions at glutamate-354 in dihydrolipoamide dehydrogenase of Escherichia coli lower the sensitivity of pyruvate dehydrogenase to NADH." Microbiology 158(Pt 5);1350-8. PMID: 22343352

Texter88: Texter FL, Radford SE, Laue ED, Perham RN, Miles JS, Guest JR (1988). "Site-directed mutagenesis and 1H NMR spectroscopy of an interdomain segment in the pyruvate dehydrogenase multienzyme complex of Escherichia coli." Biochemistry 27(1);289-96. PMID: 3280020

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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 2011-11 released on 2011-11-22 00:00:00." Database.

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

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

Wagenknecht90: Wagenknecht T, Grassucci R, Schaak D (1990). "Cryoelectron microscopy of frozen-hydrated alpha-ketoacid dehydrogenase complexes from Escherichia coli." J Biol Chem 265(36);22402-8. PMID: 2266132

Wei03: Wei W, Li H, Nemeria N, Jordan F (2003). "Expression and purification of the dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase subunits of the Escherichia coli pyruvate dehydrogenase multienzyme complex: a mass spectrometric assay for reductive acetylation of dihydrolipoamide acetyltransferase." Protein Expr Purif 28(1);140-50. PMID: 12651118

Williams90: Williams KP, Leadlay PF, Lowe PN (1990). "Inhibition of pyruvate:ferredoxin oxidoreductase from Trichomonas vaginalis by pyruvate and its analogues. Comparison with the pyruvate decarboxylase component of the pyruvate dehydrogenase complex." Biochem J 1990;268(1);69-75. PMID: 2188649

Yang85: Yang HC, Hainfeld JF, Wall JS, Frey PA (1985). "Quaternary structure of pyruvate dehydrogenase complex from Escherichia coli." J Biol Chem 1985;260(30);16049-51. PMID: 3905803

Yang86: Yang YS, Frey PA (1986). "Dihydrolipoyl transacetylase of Escherichia coli. Formation of 8-S-acetyldihydrolipoamide." Biochemistry 25(25);8173-8. PMID: 3101735

Yang94: Yang YS, Datta A, Hainfeld JF, Furuya FR, Wall JS, Frey PA (1994). "Mapping the lipoyl groups of the pyruvate dehydrogenase complex by use of gold cluster labels and scanning transmission electron microscopy." Biochemistry 33(32);9428-37. PMID: 7520749

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Zhang09a: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Cunningham98: Cunningham L, Georgellis D, Green J, Guest JR (1998). "Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterisation of an ArcA binding site in the lpd promoter." FEMS Microbiol Lett 1998;169(2);403-8. PMID: 9868788

Gohler11: Gohler AK, Kokpinar O, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C (2011). "More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli." BMC Syst Biol 5(1);197. PMID: 22168595

Ogasawara07a: Ogasawara H, Ishida Y, Yamada K, Yamamoto K, Ishihama A (2007). "PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli." J Bacteriol 189(15);5534-41. PMID: 17513468

Olvera09: Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolivar F (2009). "Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation." PLoS One 4(10);e7466. PMID: 19838295

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Quail95: Quail MA, Guest JR (1995). "Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli." Mol Microbiol 1995;15(3);519-29. PMID: 7783622

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

Sarkar08: Sarkar D, Siddiquee KA, Arauzo-Bravo MJ, Oba T, Shimizu K (2008). "Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli." Arch Microbiol 190(5);559-71. PMID: 18648770

ShalelLevanon05a: Shalel-Levanon S, San KY, Bennett GN (2005). "Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions." Biotechnol Bioeng 92(2):147-59. PMID: 15988767

Shimada11: Shimada T, Yamamoto K, Ishihama A (2011). "Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli." J Bacteriol 193(3);649-59. PMID: 21115656

Trotter11: Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J (2011). "Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment." PLoS One 6(9);e25501. PMID: 21980479

Zhang05: Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH (2005). "Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli." J Bacteriol 187(3);980-90. PMID: 15659676


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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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