aceF:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

aceF

Gene Synonym(s)

ECK0114, b0115, JW0111[1], JW0111

Product Desc.

AceF-lipoate[2][3], AceF-S-acetyldihydrolipoate[2][3]

Pyruvate dehydrogenase, dihydrolipoamide acetyltransferase E2; acetate requirement[4]

Product Synonyms(s)

pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2[1], B0115[2][1] , ECK0114, JW0111, b0115

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): aceEF[2], pdhR-aceEF-lpdA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Holoenzyme is AceE(24)+AceF(24)+Lpd(12). HT_Cmplx3_Cyt: AceF+Lpd.[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

aceF

Mnemonic

Acetate

Synonyms

ECK0114, b0115, JW0111[1], JW0111

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

BW2952

NC_012759: 125694..127586
<gbrowseImage> name=NC_012759:125694..127586 source=BW2952 preset=GeneLocation </gbrowseImage>

MG1655

2.71 minutes 

MG1655: 125695..127587
<gbrowseImage> name=NC_000913:125695..127587 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 128499..130391
<gbrowseImage> name=NC_012967:128499..130391 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 125695..127587
<gbrowseImage> name=NC_007779:125695..127587 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 99799..101691
<gbrowseImage> name=NC_010473:99799..101691 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

125698

Edman degradation

PMID:9298646


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

aceF(del) (Keio:JW0111)

deletion

deletion

Auxotrophies

PMID:16738554

Shigen

CGSC8393[5]

aceFH603C

H603C

Auxotrophies

Abolishes catalytic activity

seeded from UniProt:P06959

aceF(del)::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938

aceF(del)::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938

aceF(del)::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938

aceF(del)::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938

aceF(del)::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938

aceF(del)::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938

aceF(del)::kan

deletion

Biolog:respiration

unable to respire L-Serine

PMID:16095938

aceF10

Auxotrophies

CGSC:5708

aceF300::Tn10

Auxotrophies

CGSC:70083

aceF733(del)::kan

deletion

deletion

Auxotrophies

PMID:16738554

CGSC:99888


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0111

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCTATCGAAATCAAAGTACC

Primer 2:CCCATCACCAGACGGCGAATGTC

4D12

Kohara Phage

Genobase

PMID:3038334

4E11

Kohara Phage

Genobase

PMID:3038334

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 16% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 43% [6]

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10025

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000022

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944794

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0024

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000400

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

AceF

Synonyms

pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2[1], B0115[2][1] , ECK0114, JW0111, b0115

Product description

AceF-lipoate[2][3], AceF-S-acetyldihydrolipoate[2][3]

Pyruvate dehydrogenase, dihydrolipoamide acetyltransferase E2; acetate requirement[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0004742

dihydrolipoyllysine-residue acetyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006256

F

Seeded from EcoCyc (v14.0)

complete

GO:0004742

dihydrolipoyllysine-residue acetyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.3.1.12

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004167

F

Seeded from EcoCyc (v14.0)

complete

GO:0006096

glycolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006256

P

Seeded from EcoCyc (v14.0)

complete

GO:0006096

glycolysis

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0324

P

Seeded from EcoCyc (v14.0)

complete

GO:0031405

lipoic acid binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0450

F

Seeded from EcoCyc (v14.0)

complete

GO:0031405

lipoic acid binding

PMID:12651118

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0045254

pyruvate dehydrogenase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006256

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:16858726

IDA: Inferred from Direct Assay

C

complete

GO:0045254

pyruvate dehydrogenase complex

PMID:3903169

IDA: Inferred from Direct Assay

C

complete

GO:0045254

pyruvate dehydrogenase complex

PMID:327021

IGI: Inferred from Genetic Interaction

EcoliWiki:lpd EcoliWiki:acE


C

complete

GO:0004742

dihydrolipoyllysine-residue acetyltransferase activity

PMID:12651118

IDA: Inferred from Direct Assay

F

complete

GO:0031405

lipoic acid binding

PMID:12651118

IDA: Inferred from Direct Assay

F

Lysine at aa 425 is lipoylated

complete

Contributes to

GO:0004738

pyruvate dehydrogenase activity

PMID:3903169

IDA: Inferred from Direct Assay

F

complete

GO:0006090

pyruvate metabolic process

PMID:349114

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006086

acetyl-CoA biosynthetic process from pyruvate

PMID:349114

IMP: Inferred from Mutant Phenotype

P

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

dcm

PMID:15690043

Experiment(s):EBI-889144, EBI-894157

Protein

rpmF

PMID:16606699

Experiment(s):EBI-1135600

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1135600

Protein

lpdA

PMID:16606699

Experiment(s):EBI-1135600

Protein

rplV

PMID:16606699

Experiment(s):EBI-1135600

Protein

acnB

PMID:16606699

Experiment(s):EBI-1135600

Protein

aceE

PMID:16606699

Experiment(s):EBI-1135600

Protein

rplY

PMID:16606699

Experiment(s):EBI-1135600

Protein

rpmH

PMID:16606699

Experiment(s):EBI-1135600

Protein

mukB

PMID:16606699

Experiment(s):EBI-1135600
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

Cytoplasm

PMID:9298646

EchoLocation:aceF


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MAIEIKVPDI GADEVEITEI LVKVGDKVEA EQSLITVEGD KASMEVPSPQ AGIVKEIKVS
VGDKTQTGAL IMIFDSADGA ADAAPAQAEE KKEAAPAAAP AAAAAKDVNV PDIGSDEVEV
TEILVKVGDK VEAEQSLITV EGDKASMEVP APFAGTVKEI KVNVGDKVST GSLIMVFEVA
GEAGAAAPAA KQEAAPAAAP APAAGVKEVN VPDIGGDEVE VTEVMVKVGD KVAAEQSLIT
VEGDKASMEV PAPFAGVVKE LKVNVGDKVK TGSLIMIFEV EGAAPAAAPA KQEAAAPAPA
AKAEAPAAAP AAKAEGKSEF AENDAYVHAT PLIRRLAREF GVNLAKVKGT GRKGRILRED
VQAYVKEAIK RAEAAPAATG GGIPGMLPWP KVDFSKFGEI EEVELGRIQK ISGANLSRNW
VMIPHVTHFD KTDITELEAF RKQQNEEAAK RKLDVKITPV VFIMKAVAAA LEQMPRFNSS
LSEDGQRLTL KKYINIGVAV DTPNGLVVPV FKDVNKKGII ELSRELMTIS KKARDGKLTA
GEMQGGCFTI SSIGGLGTTH FAPIVNAPEV AILGVSKSAM EPVWNGKEFV PRLMLPISLS
FDHRVIDGAD GARFITIINN TLSDIRRLVM
Length

630

Mol. Wt

66.095 kDa

pI

5.0 (calculated)

Extinction coefficient

20,970 - 21,095 (calc based on 3 Y, 3 W, and 1 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P06959

Domain

397..630

PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)

PMID:19920124

Domain

3..74

PF00364 Biotin-requiring enzyme

PMID:19920124

Domain

106..177

PF00364 Biotin-requiring enzyme

PMID:19920124

Domain

207..278

PF00364 Biotin-requiring enzyme

PMID:19920124

Domain

325..363

PF02817 e3 binding domain

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=aceF taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128108

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944794

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000400

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P06959

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10025

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10025

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944794

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000022

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0024

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

8.02E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

850.657+/-6.457

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.2289+/-0.02836

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.906976744

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

60155

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

5226

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

28493

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

aceEF

pdhR-aceEF-lpdA

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:125675..125715 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0115 (EcoliWiki Page)

NCBI GEO profiles for aceF

microarray

GenExpDB:b0115 (EcoliWiki Page)

Summary of data for aceF from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to aceF Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10025

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0024

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0115

EcoGene

EcoGene:EG10025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000022

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000400

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000023896 (score: 1.000; bootstrap: 85%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000032195 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00026169 (score: 1.000; bootstrap: 80%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00014054 (score: 1.000; bootstrap: 82%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000003451 (score: 1.000; bootstrap: 55%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-030131-2921 (score: 1.000; bootstrap: 64%)
  • ZDB-CDNA-040425-2474 (score: 0.126)
  • ZDB-CDNA-040425-2473 (score: 0.123)
  • ZDB-GENE-040426-1539 (score: 0.123)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0230195 (score: 1.000; bootstrap: 96%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0030612 (score: 1.000; bootstrap: 59%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18998-PA (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000010123 (score: 1.000; bootstrap: 63%)

From Inparanoid:20070104

Mus musculus

  • MGI:2385311 (score: 1.000; bootstrap: 64%)
  • MGI:1351627 (score: 0.119)

From Inparanoid:20070104

Oryza gramene

  • Q655Q2 (score: 1.000; bootstrap: 51%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000032890 (score: 1.000; bootstrap: 62%)

From Inparanoid:20070104

Shigella flexneri

ACEF

From SHIGELLACYC

E. coli O157

ACEF

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Pfam (EcoliWiki Page)

PF02817 e3 binding domain

Pfam (EcoliWiki Page)

PF00364 Biotin-requiring enzyme

Pfam (EcoliWiki Page)

PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)

Pfam (EcoliWiki Page)

PF00364 Biotin-requiring enzyme

Pfam (EcoliWiki Page)

PF00364 Biotin-requiring enzyme

Superfamily (EcoliWiki Page)

SUPERFAMILY:47005

Superfamily (EcoliWiki Page)

SUPERFAMILY:51230

Superfamily (EcoliWiki Page)

SUPERFAMILY:51230

Superfamily (EcoliWiki Page)

SUPERFAMILY:51230

Panther (EcoliWiki Page)

PTHR23151:SF19

Superfamily (EcoliWiki Page)

SUPERFAMILY:52777

EcoCyc

EcoCyc:EG10025

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000022

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0024

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000400

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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