RegulonDB RegulonDB 11.1: Gene Form
   

ndh gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ndh ycfP ycfJ ArcA ArcA ArcA ArcA Fis ArcA IHF NsrR IHF PdhR FNR ArcA IHF Fis FNR Fis terminator TSS_1442 TSS_1442 ycfJp3 ycfJp3 TSS_1441 (cluster) TSS_1441 (cluster) TSS_1440 TSS_1440 ndhp ndhp TSS_1439 TSS_1439

Gene      
Name: ndh    Texpresso search in the literature
Synonym(s): ECK1095, EG10649, b1109
Genome position(nucleotides): 1166085 --> 1167389
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.95
External database links:  
ASAP:
 ABE-0003746
CGSC:
 457
ECHOBASE:
 EB0643
ECOLIHUB:
 ndh
OU-MICROARRAY:
 b1109
STRING:
 511145.b1109
COLOMBOS: ndh


Product      
Name: NADH:quinone oxidoreductase II
Synonym(s): NADH dehydrogenase II, NADH dhII, NADH-quinone reductase, NDH-2, NQR, Ndh
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 47.359
Isoelectric point: 9.194
Motif(s):
 
Type Positions Sequence Comment
2 -> 434 TTPLKKIVIVGGGAGGLEMATQLGHKLGRKKKAKITLVDRNHSHLWKPLLHEVATGSLDEGVDALSYLAHARNHGFQFQLGSVIDIDREAKTITIAELRDEKGELLVPERKIAYDTLVMALGSTSNDFNTPGVKENCIFLDNPHQARRFHQEMLNLFLKYSANLGANGKVNIAIVGGGATGVELSAELHNAVKQLHSYGYKGLTNEALNVTLVEAGERILPALPPRISAAAHNELTKLGVRVLTQTMVTSADEGGLHTKDGEYIEADLMVWAAGIKAPDFLKDIGGLETNRINQLVVEPTLQTTRDPDIYAIGDCASCPRPEGGFVPPRAQAAHQMATCAMNNILAQMNGKPLKNYQYKDHGSLVSLSNFSTVGSLMGNLTRGSMMIEGRIARFVYISLYRMHQIALHGYFKTGLMMLVGSINRVIRPRLKLH UniProt: Type II NADH:quinone oxidoreductase.
6 -> 121 KKIVIVGGGAGGLEMATQLGHKLGRKKKAKITLVDRNHSHLWKPLLHEVATGSLDEGVDALSYLAHARNHGFQFQLGSVIDIDREAKTITIAELRDEKGELLVPERKIAYDTLVMA FAD binding domain
7 -> 42 KIVIVGGGAGGLEMATQLGHKLGRKKKAKITLVDRN
12 -> 16 GGGAG UniProt: FAD.
170 -> 278 KVNIAIVGGGATGVELSAELHNAVKQLHSYGYKGLTNEALNVTLVEAGERILPALPPRISAAAHNELTKLGVRVLTQTMVTSADEGGLHTKDGEYIEADLMVWAAGIKA NADH binding region

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.6 - aerobic respiration
  1 - metabolism --> 1.4 - energy production/transport --> 1.4.1 - electron donors
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0030964 - NADH dehydrogenase complex
molecular_function GO:0016491 - oxidoreductase activity
GO:0050660 - flavin adenine dinucleotide binding
GO:0003954 - NADH dehydrogenase activity
GO:0008137 - NADH dehydrogenase (ubiquinone) activity
GO:0050136 - NADH dehydrogenase (quinone) activity
biological_process GO:0006116 - NADH oxidation
GO:0009060 - aerobic respiration
GO:0009061 - anaerobic respiration
GO:0055070 - copper ion homeostasis
GO:0019646 - aerobic electron transport chain
Note(s): Note(s): ...[more].
Reference(s): [1] Helling RB. 2002
[2] Noguchi Y., et al., 2004
[3] Yagi T. 1991
External database links:  
ALPHAFOLD:
 P00393
DIP:
 DIP-10325N
ECOCYC:
 NADH-DHII-MONOMER
ECOLIWIKI:
 b1109
INTERPRO:
 IPR023753
INTERPRO:
 IPR036188
MODBASE:
 P00393
PDB:
 1OZK
PFAM:
 PF07992
PRIDE:
 P00393
PRODB:
 PRO_000023365
REFSEQ:
 NP_415627
SMR:
 P00393
UNIPROT:
 P00393


Operon      
Name: ndh         
Operon arrangement:
Transcription unit        Promoter
ndh


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: NsrR, Fur, FNR, IHF, ArcA, Fis, PdhR


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_1439 1165531 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1440 1166052 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1441 (cluster) 1166069 forward nd [RS-EPT-CBR] [4]
  promoter ycfJp3 1167407 forward nd [COMP-AINF] [5]
  promoter TSS_1442 1168035 forward nd [RS-EPT-CBR] [4]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Helling RB., 2002, Speed versus efficiency in microbial growth and the role of parallel pathways., J Bacteriol 184(4):1041-5

 [2] Noguchi Y., Nakai Y., Shimba N., Toyosaki H., Kawahara Y., Sugimoto S., Suzuki E., 2004, The energetic conversion competence of Escherichia coli during aerobic respiration studied by 31P NMR using a circulating fermentation system., J Biochem 136(4):509-15

 [3] Yagi T., 1991, Bacterial NADH-quinone oxidoreductases., J Bioenerg Biomembr 23(2):211-25

 [4] 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.

 [5] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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