RegulonDB RegulonDB 10.7: Gene Form
   

pdxK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pdxK crr yfeK pdxKp1 pdxKp1 yfeKp yfeKp TSS_2733 (cluster) TSS_2733 (cluster) TSS_2732 TSS_2732 TSS_2731 TSS_2731

Gene      
Name: pdxK    Texpresso search in the literature
Synonym(s): ECK2413, G7259, b2418, pdxL, thiJ, yfeI
Genome position(nucleotides): 2536386 <-- 2537237 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.23
External database links:  
ASAP:
ABE-0007973
ECHOBASE:
EB2519
OU-MICROARRAY:
b2418
PORTECO:
pdxK
REGULONDB:
b2418
STRING:
511145.b2418
M3D: pdxK
COLOMBOS: pdxK
PortEco: b2418


Product      
Name: pyridoxal kinase I
Synonym(s): PLK1, PdxK, PdxL, ThiJ, YfeI
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.847
Isoelectric point: 4.965
Motif(s):
 
Type Positions Sequence
88 -> 265 QLRAVTTGYMGTASQIKILAEWLTALRKDHPDLLIMVDPVIGDIDSGIYVKPDLPEAYRQYLLPLAQGITPNIFELEILTGKNCRDLDSAIAAAKSLLSDTLKWVVVTSASGNEENQEMQVVVVTADSVNVISHSRVKTDLKGTGDLFCAQLISGLLKGKALTDAVHRAGLRVLEVMR
221 -> 224 HSRV

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.27 - pyridoxal 5'-phosphate salvage
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0016301 - kinase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0030170 - pyridoxal phosphate binding
GO:0008270 - zinc ion binding
GO:0008478 - pyridoxal kinase activity
GO:0008902 - hydroxymethylpyrimidine kinase activity
GO:0000287 - magnesium ion binding
GO:0030955 - potassium ion binding
GO:0042803 - protein homodimerization activity
biological_process GO:0008615 - pyridoxine biosynthetic process
GO:0009443 - pyridoxal 5'-phosphate salvage
GO:0016310 - phosphorylation
Note(s): Note(s): ...[more].
Reference(s): [1] Furukawa Y., et al., 1981
[2] Mizote T., et al., 1989
[3] Yamada R., et al., 1981
[4] Yamada RH., et al., 1980
[5] Yang Y., et al., 1996
[6] Zhao G., et al., 1996
External database links:  
ECOCYC:
PDXK-MONOMER
ECOLIWIKI:
b2418
INTERPRO:
IPR023479
INTERPRO:
IPR013749
INTERPRO:
IPR029056
INTERPRO:
IPR004625
MODBASE:
P40191
PANTHER:
PTHR10534
PDB:
2DDW
PDB:
2DDO
PDB:
2DDM
PFAM:
PF08543
PRIDE:
P40191
PRODB:
PRO_000023506
PROTEINMODELPORTAL:
P40191
REFSEQ:
NP_416913
SMR:
P40191
UNIPROT:
P40191


Operon      
Name: pdxK         
Operon arrangement:
Transcription unit        Promoter
pdxK


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_2731 2535839 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2732 2536064 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2733 (cluster) 2537277 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [7]


Evidence    

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



Reference(s)    

 [1] Furukawa Y., Yamada R., Iwashima A., 1981, Inactivation of microbial pyridoxal kinase by pyridoxal., Acta Vitaminol Enzymol 3(3):145-56

 [2] Mizote T., Nakayama H., 1989, Purification and properties of hydroxymethylpyrimidine kinase from Escherichia coli., Biochim Biophys Acta 991(1):109-13

 [3] Yamada R., Furukawa Y., 1981, Role of pyridoxal kinase in vitamin B6 uptake by Escherichia coli., J Nutr Sci Vitaminol (Tokyo) 27(3):177-91

 [4] Yamada RH., Furukawa Y., 1980, Apparent pyridoxine transport mutants of Escherichia coli with pyridoxal kinase deficiency., Biochim Biophys Acta 600(2):581-4

 [5] Yang Y., Zhao G., Winkler ME., 1996, Identification of the pdxK gene that encodes pyridoxine (vitamin B6) kinase in Escherichia coli K-12., FEMS Microbiol Lett 141(1):89-95

 [6] Zhao G., Winkler ME., 1996, 4-Phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12., FEMS Microbiol Lett 135(2-3):275-80

 [7] 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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