RegulonDB RegulonDB 10.9: Gene Form
   

nikA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nikA nikB nikC acpT NikR FNR terminator anti-terminator anti-anti-terminator TSS_4084 TSS_4084 TSS_4083 (cluster) TSS_4083 (cluster) TSS_4082 TSS_4082 TSS_4081 TSS_4081 TSS_4080 (cluster) TSS_4080 (cluster) TSS_4079 TSS_4079 nikAp1 nikAp1 nikAp2 nikAp2

Gene      
Name: nikA    Texpresso search in the literature
Synonym(s): ECK3460, EG12075, b3476, hydC, hydD
Genome position(nucleotides): 3613667 --> 3615241 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.33
External database links:  
ASAP:
ABE-0011354
CGSC:
18226
ECHOBASE:
EB2000
ECOLIHUB:
nikA
OU-MICROARRAY:
b3476
STRING:
511145.b3476
COLOMBOS: nikA


Product      
Name: Ni(2+) ABC transporter periplasmic binding protein
Synonym(s): HydC, HydD, NikA
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,periplasmic space
Molecular weight: 58.719
Isoelectric point: 5.995
Motif(s):
 
Type Positions Sequence
1 -> 22 MLSTLRRTLFALLACASFIVHA
68 -> 433 VIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSM
438 -> 438 H
23 -> 524 AAPDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPVKP

 

Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.1 - The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases --> 4.3.A.1.p - ABC superfamily, periplasmic binding component
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
GO:0043190 - ATP-binding cassette (ABC) transporter complex
molecular_function GO:0046914 - transition metal ion binding
GO:0005515 - protein binding
GO:0016151 - nickel cation binding
GO:0051540 - metal cluster binding
GO:0020037 - heme binding
GO:1904680 - peptide transmembrane transporter activity
biological_process GO:0015833 - peptide transport
GO:0015675 - nickel cation transport
GO:0055085 - transmembrane transport
GO:0050919 - negative chemotaxis
Note(s): Note(s): ...[more].
Reference(s): [1] Addy C., et al., 2007
External database links:  
DIP:
DIP-10340N
ECOCYC:
NIKA-MONOMER
ECOLIWIKI:
b3476
INTERPRO:
IPR030678
INTERPRO:
IPR039424
INTERPRO:
IPR000914
INTERPRO:
IPR011980
INTERPRO:
IPR023765
MODBASE:
P33590
PANTHER:
PTHR30290
PDB:
3MVY
PDB:
6R4Q
PDB:
5ON9
PDB:
5ON8
PDB:
5ON5
PDB:
5ON4
PDB:
5ON1
PDB:
1UIU
PDB:
1UIV
PDB:
1ZLQ
PDB:
2NOO
PDB:
3DP8
PDB:
3E3K
PDB:
3MVW
PDB:
3MVX
PDB:
3MVZ
PDB:
3MW0
PDB:
3MZ9
PDB:
3MZB
PDB:
3QIM
PDB:
4DCX
PDB:
4DCY
PDB:
4I8C
PDB:
4I9D
PDB:
5L8D
PDB:
5MWU
PDB:
5ON0
PFAM:
PF00496
PRIDE:
P33590
PRODB:
PRO_000023384
PROSITE:
PS01040
REFSEQ:
NP_417933
SMR:
P33590
UNIPROT:
P33590


Operon      
Name: nikABCDER         
Operon arrangement:
Transcription unit        Promoter
nikABCDER
nikABCDER
nikR


Transcriptional Regulation      
Display Regulation             
Activated by: FNR
Repressed by: NarL, NikR


RNA cis-regulatory element    
Attenuation: Transcriptional


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_4079 3615136 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4080 (cluster) 3615142 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_4081 3616046 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4082 3616409 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4083 (cluster) 3616882 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_4084 3616908 forward nd [RS-EPT-CBR] [2]


Evidence    

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



Reference(s)    

 [1] Addy C., Ohara M., Kawai F., Kidera A., Ikeguchi M., Fuchigami S., Osawa M., Shimada I., Park SY., Tame JR., Heddle JG., 2007, Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography., Acta Crystallogr D Biol Crystallogr 63(Pt 2):221-9

 [2] 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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