RegulonDB RegulonDB 11.1: Gene Form
   

ndk gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pbpC rlmN ndk terminator ndkp4 ndkp4 TSS_2818 TSS_2818 TSS_2817 TSS_2817

Gene      
Name: ndk    Texpresso search in the literature
Synonym(s): ECK2514, EG10650, b2518
Genome position(nucleotides): 2644433 <-- 2644864
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.31
External database links:  
ASAP:
 ABE-0008291
CGSC:
 32926
ECHOBASE:
 EB0644
ECOLIHUB:
 ndk
OU-MICROARRAY:
 b2518
STRING:
 511145.b2518
COLOMBOS: ndk


Product      
Name: nucleoside diphosphate kinase
Synonym(s): Ndk
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 15.463
Isoelectric point: 5.626
Motif(s):
 
Type Positions Sequence Comment
2 -> 143 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR UniProt: Nucleoside diphosphate kinase.
4 -> 137 ERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGE
119 -> 119 S UniProt: Still autophosphorylates. No change in kinase activity..
121 -> 121 S UniProt: Still autophosphorylates. No change in kinase activity..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.2 - nucleotides --> 1.5.2.3 - purine ribonucleotide biosynthesis
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.33 - nucleotide and nucleoside conversions
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0016301 - kinase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0004550 - nucleoside diphosphate kinase activity
GO:0042802 - identical protein binding
biological_process GO:0006163 - purine nucleotide metabolic process
GO:0009117 - nucleotide metabolic process
GO:0006220 - pyrimidine nucleotide metabolic process
GO:0006241 - CTP biosynthetic process
GO:0016310 - phosphorylation
GO:0006183 - GTP biosynthetic process
GO:0006228 - UTP biosynthetic process
GO:0006165 - nucleoside diphosphate phosphorylation
External database links:  
ALPHAFOLD:
 P0A763
DIP:
 DIP-31870N
ECOCYC:
 NUCLEOSIDE-DIP-KIN-MONOMER
ECOLIWIKI:
 b2518
INTERPRO:
 IPR034907
INTERPRO:
 IPR036850
INTERPRO:
 IPR023005
INTERPRO:
 IPR001564
PDB:
 2hur
PFAM:
 PF00334
PRIDE:
 P0A763
PRINTS:
 PR01243
PRODB:
 PRO_000023366
PROSITE:
 PS00469
REFSEQ:
 NP_417013
SMART:
 SM00562
SMR:
 P0A763
SWISSMODEL:
 P0A763
UNIPROT:
 P0A763


Operon      
Name: ndk         
Operon arrangement:
Transcription unit        Promoter
ndk


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_2817 2644379 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2818 2644913 reverse nd [RS-EPT-CBR] [1]
  promoter ndkp4 2644960 reverse nd [COMP-AINF] [2]


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] 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.

 [2] 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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