RegulonDB RegulonDB 11.1: Gene Form
   

pdxA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lptD surA pdxA rsmA apaG TSS_109 TSS_109 TSS_108 (cluster) TSS_108 (cluster) TSS_107 TSS_107 TSS_106 TSS_106 TSS_105 TSS_105 TSS_104 TSS_104 TSS_103 (cluster) TSS_103 (cluster) TSS_102 (cluster) TSS_102 (cluster) TSS_101 TSS_101 TSS_100 TSS_100 TSS_99 TSS_99 TSS_98 TSS_98 TSS_97 TSS_97 TSS_96 (cluster) TSS_96 (cluster) TSS_95 TSS_95 TSS_94 TSS_94 TSS_93 TSS_93 TSS_92 TSS_92 TSS_91 TSS_91 TSS_90 TSS_90 rsmAp rsmAp TSS_89 TSS_89 TSS_88 TSS_88 TSS_87 (cluster) TSS_87 (cluster) TSS_86 TSS_86 apaGp apaGp TSS_84 TSS_84 apaHp4 apaHp4

Gene      
Name: pdxA    Texpresso search in the literature
Synonym(s): ECK0053, EG10691, b0052
Genome position(nucleotides): 52427 <-- 53416
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 56.36
External database links:  
ASAP:
 ABE-0000178
CGSC:
 420
ECHOBASE:
 EB0685
ECOLIHUB:
 pdxA
NCBI-GENE:
 944919
OU-MICROARRAY:
 b0052
STRING:
 511145.b0052
COLOMBOS: pdxA


Product      
Name: 4-hydroxythreonine-4-phosphate dehydrogenase
Synonym(s): PdxA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 35.114
Isoelectric point: 6.287
Motif(s):
 
Type Positions Sequence Comment
34 -> 321 LVVCADATLLTNRAAMLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVLNELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLA

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.6 - pyridoxal 5'phosphate
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0008270 - zinc ion binding
GO:0050570 - 4-hydroxythreonine-4-phosphate dehydrogenase activity
GO:0000287 - magnesium ion binding
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0050897 - cobalt ion binding
GO:0051287 - NAD binding
biological_process GO:0008615 - pyridoxine biosynthetic process
GO:0042823 - pyridoxal phosphate biosynthetic process
External database links:  
ALPHAFOLD:
 P19624
DIP:
 DIP-10448N
ECOCYC:
 PDXA-MONOMER
ECOLIWIKI:
 b0052
INTERPRO:
 IPR005255
INTERPRO:
 IPR037510
MODBASE:
 P19624
PANTHER:
 PTHR30004
PDB:
 1PS6
PDB:
 1PTM
PDB:
 1PS7
PFAM:
 PF04166
PRIDE:
 P19624
PRODB:
 PRO_000023502
REFSEQ:
 NP_414594
SMR:
 P19624
UNIPROT:
 P19624


Operon      
Name: lptD-surA-pdxA-rsmA-apaGH         
Operon arrangement:
Transcription unit        Promoter
apaGH
rsmA-apaGH
imp
imp
imp-surA-pdxA
pdxA-rsmA
pdxA-rsmA-apaGH
surA-pdxA-rsmA-apaGH


Transcriptional Regulation      
Display Regulation             
Activated by: Fis


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 apaHp4 51293 reverse nd [COMP-AINF] [1]
  promoter TSS_84 51998 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_86 52194 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_87 (cluster) 52478 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_88 52548 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_89 52587 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_90 53904 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_91 54275 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_92 54363 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_93 54605 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_94 54746 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_95 54754 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_96 (cluster) 54762 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_97 54765 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_98 54884 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_99 55120 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_100 55146 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_101 55785 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_102 (cluster) 55791 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_103 (cluster) 55800 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_104 55908 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_105 55916 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_106 55920 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_107 56036 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_108 (cluster) 56466 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_109 56724 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] 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

 [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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