RegulonDB

Gene
Name:	aceF
Synonym(s):	ECK0114, EG10025, b0115
Genome position(nucleotides):	125695 --> 127587
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.68
External database links:

ASAP:	ABE-0000400
CGSC:	26530
ECHOBASE:	EB0024
ECOLIHUB:	aceF
MIM:	248600
OU-MICROARRAY:	b0115
STRING:	511145.b0115
COLOMBOS:	aceF

Gene

Name:

aceF

Synonym(s):

ECK0114, EG10025, b0115

Genome position(nucleotides):

125695 --> 127587

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.68

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

MIM:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

2 -> 630

AIEIKVPDIGADEVEITEILVKVGDKVEAEQSLITVEGDKASMEVPSPQAGIVKEIKVSVGDKTQTGALIMIFDSADGAADAAPAQAEEKKEAAPAAAPAAAAAKDVNVPDIGSDEVEVTEILVKVGDKVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVNVGDKVSTGSLIMVFEVAGEAGAAAPAAKQEAAPAAAPAPAAGVKEVNVPDIGGDEVEVTEVMVKVGDKVAAEQSLITVEGDKASMEVPAPFAGVVKELKVNVGDKVKTGSLIMIFEVEGAAPAAAPAKQEAAAPAPAAKAEAPAAAPAAKAEGKSEFAENDAYVHATPLIRRLAREFGVNLAKVKGTGRKGRILREDVQAYVKEAIKRAEAAPAATGGGIPGMLPWPKVDFSKFGEIEEVELGRIQKISGANLSRNWVMIPHVTHFDKTDITELEAFRKQQNEEAAKRKLDVKITPVVFIMKAVAAALEQMPRFNSSLSEDGQRLTLKKYINIGVAVDTPNGLVVPVFKDVNKKGIIELSRELMTISKKARDGKLTAGEMQGGCFTISSIGGLGTTHFAPIVNAPEVAILGVSKSAMEPVWNGKEFVPRLMLPISLSFDHRVIDGADGARFITIINNTLSDIRRLVM

UniProt: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex.

4 -> 73

EIKVPDIGADEVEITEILVKVGDKVEAEQSLITVEGDKASMEVPSPQAGIVKEIKVSVGDKTQTGALIMI

105 -> 178

AKDVNVPDIGSDEVEVTEILVKVGDKVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVNVGDKVSTGSLIMVFE

UniProt: Lipoyl-binding 2.

107 -> 176

DVNVPDIGSDEVEVTEILVKVGDKVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVNVGDKVSTGSLIMV

206 -> 279

VKEVNVPDIGGDEVEVTEVMVKVGDKVAAEQSLITVEGDKASMEVPAPFAGVVKELKVNVGDKVKTGSLIMIFE

UniProt: Lipoyl-binding 3.

Type

Positions

Sequence

Comment

2 -> 630

UniProt: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex.

4 -> 73

EIKVPDIGADEVEITEILVKVGDKVEAEQSLITVEGDKASMEVPSPQAGIVKEIKVSVGDKTQTGALIMI

105 -> 178

AKDVNVPDIGSDEVEVTEILVKVGDKVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVNVGDKVSTGSLIMVFE

UniProt: Lipoyl-binding 2.

107 -> 176

DVNVPDIGSDEVEVTEILVKVGDKVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVNVGDKVSTGSLIMV

206 -> 279

VKEVNVPDIGGDEVEVTEVMVKVGDKVAAEQSLITVEGDKASMEVPAPFAGVVKELKVNVGDKVKTGSLIMIFE

UniProt: Lipoyl-binding 3.

207 -> 277

KEVNVPDIGGDEVEVTEVMVKVGDKVAAEQSLITVEGDKASMEVPAPFAGVVKELKVNVGDKVKTGSLIMI

327 -> 362

VHATPLIRRLAREFGVNLAKVKGTGRKGRILREDVQ

328 -> 365

HATPLIRRLAREFGVNLAKVKGTGRKGRILREDVQAYV

UniProt: Peripheral subunit-binding (PSBD).

373 -> 389

EAAPAATGGGIPGMLPW

UniProt: Hydrophobic; Sequence Annotation Type: region of interest.

399 -> 629

EIEEVELGRIQKISGANLSRNWVMIPHVTHFDKTDITELEAFRKQQNEEAAKRKLDVKITPVVFIMKAVAAALEQMPRFNSSLSEDGQRLTLKKYINIGVAVDTPNGLVVPVFKDVNKKGIIELSRELMTISKKARDGKLTAGEMQGGCFTISSIGGLGTTHFAPIVNAPEVAILGVSKSAMEPVWNGKEFVPRLMLPISLSFDHRVIDGADGARFITIINNTLSDIRRLV

542 -> 567

EMQGGCFTISSIGGLGTTHFAPIVNA

UniProt: Hydrophobic; Sequence Annotation Type: region of interest.

603 -> 603

UniProt: Abolishes catalytic activity..

Multifun Terms (GenProtEC)

1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds

1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.3 - pyruvate dehydrogenase

1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.21 - glyoxylate degradation

Gene Ontology Terms (GO)

cellular_component

GO:0005737 - cytoplasm
GO:0045254 - pyruvate dehydrogenase complex

molecular_function

GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0016407 - acetyltransferase activity
GO:0016746 - acyltransferase activity
GO:0004738 - pyruvate dehydrogenase activity
GO:0004742 - dihydrolipoyllysine-residue acetyltransferase activity
GO:0030523 - dihydrolipoamide S-acyltransferase activity
GO:0031405 - lipoic acid binding

biological_process

GO:0006086 - acetyl-CoA biosynthetic process from pyruvate
GO:0006090 - pyruvate metabolic process
GO:0006096 - glycolytic process
GO:0042867 - pyruvate catabolic process

Transcriptional Regulation
	Display Regulation
Activated by:	CRP, FNR
Repressed by:	NsrR, FNR, Cra, ArcA, BtsR, PdhR

Transcriptional Regulation

Display Regulation

Activated by:

CRP, FNR

Repressed by:

NsrR, FNR, Cra, ArcA, BtsR, PdhR

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_241	123388	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_242 (cluster)	123471	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_243	124973	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_244	125226	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_245	125425	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_246	127432	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_247	127436	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_248	127896	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_249	127898	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_250	127900	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_251	127907	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_252	127929	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_253	127953	forward	nd	[RS-EPT-CBR]	[14]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_241

123388

forward

[RS-EPT-CBR]

[14]

promoter

TSS_242 (cluster)

123471

forward

[RS-EPT-CBR]

[14]

promoter

TSS_243

124973

forward

[RS-EPT-CBR]

[14]

promoter

TSS_244

125226

forward

[RS-EPT-CBR]

[14]

promoter

TSS_245

125425

forward

[RS-EPT-CBR]

[14]

promoter

TSS_246

127432

forward

[RS-EPT-CBR]

[14]

promoter

TSS_247

127436

forward

[RS-EPT-CBR]

[14]

promoter

TSS_248

127896

forward

[RS-EPT-CBR]

[14]

promoter

TSS_249

127898

forward

[RS-EPT-CBR]

[14]

promoter

TSS_250

127900

forward

[RS-EPT-CBR]

[14]

promoter

TSS_251

127907

forward

[RS-EPT-CBR]

[14]

promoter

TSS_252

127929

forward

[RS-EPT-CBR]

[14]

promoter

TSS_253

127953

forward

[RS-EPT-CBR]

[14]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] 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
[2] 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 19(18):4208-13
[3] 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
[4] 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
[5] 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
[6] 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
[7] 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
[8] 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
[9] 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
[10] 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
[11] 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
[12] 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
[13] Yang YS., Frey PA., 1986, Dihydrolipoyl transacetylase of Escherichia coli. Formation of 8-S-acetyldihydrolipoamide., Biochemistry 25(25):8173-8
[14] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] 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

[2] 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 19(18):4208-13

[3] 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

[4] 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

[5] 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

[6] 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

[7] 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

[8] 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

[9] 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

[10] 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

[11] 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

[12] 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

[13] Yang YS., Frey PA., 1986, Dihydrolipoyl transacetylase of Escherichia coli. Formation of 8-S-acetyldihydrolipoamide., Biochemistry 25(25):8173-8

[14] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.