RegulonDB RegulonDB 11.1: Gene Form
   

pdxH gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

tyrS pdxH mliC anti-anti-terminator anti-terminator terminator terminator pdxHp pdxHp TSS_1915 TSS_1915 TSS_1914 TSS_1914 tyrSp2 tyrSp2 tyrSp1 tyrSp1 TSS_1913 TSS_1913

Gene      
Name: pdxH    Texpresso search in the literature
Synonym(s): ECK1634, EG11487, b1638
Genome position(nucleotides): 1717351 <-- 1718007
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.9
External database links:  
ASAP:
 ABE-0005482
CGSC:
 417
ECHOBASE:
 EB1450
ECOLIHUB:
 pdxH
MIM:
 610090
NCBI-GENE:
 946806
OU-MICROARRAY:
 b1638
STRING:
 511145.b1638
COLOMBOS: pdxH


Product      
Name: pyridoxine/pyridoxamine 5'-phosphate oxidase
Synonym(s): PdxH, pyridoxal 5-phosphate synthase
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 25.545
Isoelectric point: 9.604
Motif(s):
 
Type Positions Sequence Comment
2 -> 218 SDNDELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP UniProt: Pyridoxine/pyridoxamine 5'-phosphate oxidase.
14 -> 17 RREY UniProt: Substrate binding; Sequence Annotation Type: region of interest.
17 -> 17 Y UniProt: Reduces affinity for substrate 3-fold, but has about 5-fold increase in catalytic activity..
40 -> 122 SQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLS
49 -> 49 D UniProt: Reduces affinity for substrate 3-fold and catalytic activity 2-fold..

 
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
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.27 - pyridoxal 5'-phosphate salvage
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0032991 - protein-containing complex
molecular_function GO:1902444 - riboflavin binding
GO:0016491 - oxidoreductase activity
GO:0016638 - oxidoreductase activity, acting on the CH-NH2 group of donors
GO:0030170 - pyridoxal phosphate binding
GO:0004733 - pyridoxamine-phosphate oxidase activity
GO:0010181 - FMN binding
GO:0042803 - protein homodimerization activity
GO:0042301 - phosphate ion binding
biological_process GO:0042816 - vitamin B6 metabolic process
GO:0008615 - pyridoxine biosynthetic process
GO:0042823 - pyridoxal phosphate biosynthetic process
GO:0036001 - 'de novo' pyridoxal 5'-phosphate biosynthetic process
External database links:  
ALPHAFOLD:
 P0AFI7
DIP:
 DIP-48024N
ECOCYC:
 PDXH-MONOMER
ECOLIWIKI:
 b1638
INTERPRO:
 IPR000659
INTERPRO:
 IPR011576
INTERPRO:
 IPR019740
INTERPRO:
 IPR019576
INTERPRO:
 IPR012349
MODBASE:
 P0AFI7
PANTHER:
 PTHR10851
PDB:
 1WV4
PDB:
 1JNW
PDB:
 1G79
PDB:
 1G78
PDB:
 1G77
PDB:
 1DNL
PDB:
 1G76
PFAM:
 PF01243
PFAM:
 PF10590
PRIDE:
 P0AFI7
PRODB:
 PRO_000023504
PROSITE:
 PS01064
REFSEQ:
 NP_416155
SMR:
 P0AFI7
SWISSMODEL:
 P0AFI7
UNIPROT:
 P0AFI7


Operon      
Name: pdxH-tyrS-pdxY         
Operon arrangement:
Transcription unit        Promoter
tyrS-pdxY
tyrS-pdxY
pdxH-tyrS-pdxY
pdxY


RNA cis-regulatory element    
Attenuation: Translational


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_1913 1716884 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1914 1717287 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1915 1717731 reverse nd [RS-EPT-CBR] [1]


Evidence    

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


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.

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