RegulonDB RegulonDB 11.1: 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
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 Comment
1 -> 22 MLSTLRRTLFALLACASFIVHA
23 -> 524 AAPDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPVKP UniProt: Nickel-binding periplasmic protein.
68 -> 433 VIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSM
438 -> 438 H H → I: significant decrease in nickel uptake and in [NiFe] hydrogenase activity in vivo

 
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:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
GO:0043190 - ATP-binding cassette (ABC) transporter complex
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
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:0098716 - nickel cation import across plasma membrane
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:  
ALPHAFOLD:
 P33590
DIP:
 DIP-10340N
ECOCYC:
 NIKA-MONOMER
ECOLIWIKI:
 b3476
INTERPRO:
 IPR011980
INTERPRO:
 IPR023765
INTERPRO:
 IPR030678
INTERPRO:
 IPR039424
INTERPRO:
 IPR000914
MODBASE:
 P33590
PANTHER:
 PTHR30290
PDB:
 3MZB
PDB:
 3QIM
PDB:
 4DCX
PDB:
 4DCY
PDB:
 4I8C
PDB:
 4I9D
PDB:
 5L8D
PDB:
 5MWU
PDB:
 5ON0
PDB:
 5ON1
PDB:
 5ON4
PDB:
 5ON5
PDB:
 5ON8
PDB:
 5ON9
PDB:
 6R4Q
PDB:
 7A0C
PDB:
 3MZ9
PDB:
 3MW0
PDB:
 3MVZ
PDB:
 3MVY
PDB:
 3MVX
PDB:
 3MVW
PDB:
 3E3K
PDB:
 3DP8
PDB:
 2NOO
PDB:
 1ZLQ
PDB:
 1UIV
PDB:
 1UIU
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 nd [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 nd [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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