RegulonDB RegulonDB 10.8: Gene Form
   

lpd gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

aceF yacH lpd ArcA CRP ArcA Fis TSS_254 TSS_254 TSS_253 TSS_253 TSS_252 TSS_252 TSS_251 TSS_251 TSS_250 TSS_250 TSS_249 TSS_249 TSS_248 TSS_248 lpdAp lpdAp TSS_247 TSS_247 TSS_246 TSS_246

Gene      
Name: lpd    Texpresso search in the literature
Synonym(s): ECK0115, EG10543, b0116, dhl, lpdA
Genome position(nucleotides): 127912 --> 129336 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.05
External database links:  
ASAP:
 ABE-0000404
CGSC:
 544
ECHOBASE:
 EB0538
ECOO157CYC:
 LPDA
MIM:
 246900
NCBI-GENE:
 944854
OU-MICROARRAY:
 b0116
PortEco:
 lpd
STRING:
 511145.b0116
COLOMBOS: lpd


Product      
Name: lipoamide dehydrogenase
Synonym(s): Dhl, E3 subunit, Lpd, LpdA
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol
Molecular weight: 50.688
Isoelectric point: 6.071
Motif(s):
 
Type Positions Sequence
2 -> 474 STEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTAVEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWVGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK
270 -> 273 AIGR
347 -> 455 IPSIAYTEPEVAWVGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLA
182 -> 186 GGGII
8 -> 328 QVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTAVEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPHIFAIGDIVGQPMLAHKGVHEG

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.3 - amino acids
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.3 - pyruvate dehydrogenase
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.17 - formyl-THF biosynthesis
Gene Ontology Terms (GO)  
cellular_component GO:0005623 - cell
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005960 - glycine cleavage complex
GO:0045248 - cytosolic oxoglutarate dehydrogenase complex
GO:0045250 - cytosolic pyruvate dehydrogenase complex
GO:0005886 - plasma membrane
molecular_function GO:0005515 - protein binding
GO:0016491 - oxidoreductase activity
GO:0008270 - zinc ion binding
GO:0050660 - flavin adenine dinucleotide binding
GO:0004148 - dihydrolipoyl dehydrogenase activity
GO:0016668 - oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0015036 - disulfide oxidoreductase activity
GO:0042802 - identical protein binding
biological_process GO:0006090 - pyruvate metabolic process
GO:0006096 - glycolytic process
GO:0006979 - response to oxidative stress
GO:0019464 - glycine decarboxylation via glycine cleavage system
GO:0045454 - cell redox homeostasis
GO:0055114 - oxidation-reduction process
GO:0006103 - 2-oxoglutarate metabolic process
External database links:  
DIP:
 DIP-6854N
ECOCYC:
 E3-MONOMER
ECOLIWIKI:
 b0116
INTERPRO:
 IPR001100
INTERPRO:
 IPR036188
INTERPRO:
 IPR023753
INTERPRO:
 IPR016156
INTERPRO:
 IPR012999
INTERPRO:
 IPR006258
INTERPRO:
 IPR004099
MINT:
 MINT-1242510
MODBASE:
 P0A9P0
PANTHER:
 PTHR22912:SF20
PDB:
 4JDR
PFAM:
 PF02852
PFAM:
 PF07992
PRIDE:
 P0A9P0
PRINTS:
 PR00368
PRODB:
 PRO_000023109
PROSITE:
 PS00076
REFSEQ:
 NP_414658
SMR:
 P0A9P0
SWISSMODEL:
 P0A9P0
UNIPROT:
 P0A9P0


Operon      
Name: pdhR-aceEF-lpd         
Operon arrangement:
Transcription unit        Promoter
pdhR-aceEF-lpdA
aceEF
lpdA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, Fur, FNR, Fis
Repressed by: CRP, Fur, FNR, Cra, ArcA, PdhR, BtsR
Growth Conditions:

[1] 

C: Escherichia coli| minimal medium| glucose 11 mM| OD650 of 0.2
E: Escherichia coli| pdhR knockout mutant| minimal medium| glucose 11 mM| OD650 of 0.2

[2] 

C: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| OD650 of 0.2
E: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| glucose 10 mM| OD650 of 0.2

[3] 

C: Escherichia coli| minimal medium| pyruvate 40 mM| OD650 of 0.2
E: Escherichia coli| pdhR knockout mutant| minimal medium| pyruvate 40 mM| OD650 of 0.2

[4] 

C: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| OD650 of 0.2
E: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| pyruvate 40 mM| OD650 of 0.2

[5] 

C: Escherichia coli| pdhR knockout mutant| minimal medium| glucose 11 mM| OD650 of 0.2
E: Escherichia coli| pdhR knockout mutant; multicopy plasmid pGS613 (pdhR) mutant| minimal medium| glucose 11 mM| OD650 of 0.2

[6] 

C: Escherichia coli| arcA knockout mutant; multicopy plasmid pRB38 (arcA) mutant| L broth| glucose 11 mM| OD650 of 0.4
E: Escherichia coli| arcA knockout mutant| L broth| glucose 11 mM| OD650 of 0.4

[7] 

C: Escherichia coli| pdhR knockout mutant| minimal medium| pyruvate 40 mM| OD650 of 0.2
E: Escherichia coli| pdhR knockout mutant; multicopy plasmid pGS613 (pdhR) mutant| minimal medium| pyruvate 40 mM| OD650 of 0.2


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_246 127432 forward nd [RS-EPT-CBR] [1]
  promoter TSS_247 127436 forward nd [RS-EPT-CBR] [1]
  promoter TSS_248 127896 forward nd [RS-EPT-CBR] [1]
  promoter TSS_249 127898 forward nd [RS-EPT-CBR] [1]
  promoter TSS_250 127900 forward nd [RS-EPT-CBR] [1]
  promoter TSS_251 127907 forward nd [RS-EPT-CBR] [1]
  promoter TSS_252 127929 forward nd [RS-EPT-CBR] [1]
  promoter TSS_253 127953 forward nd [RS-EPT-CBR] [1]
  promoter TSS_254 130229 forward nd [RS-EPT-CBR] [1]


Evidence    

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


Reference(s)    

 [1] 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.

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