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XapR DNA-binding transcriptional activator

Synonyms: XapR, XapR-xanthosine
Summary:
XapR, "xanthosine phosphorylase regulator," activates transcription of genes involved in xanthosine metabolism when xanthosine is present [1, 2] Deoxyinosine can also induce XapR activity, although not to the same extent as xanthosine [1]. XapR, which belongs to the LysR family of transcriptional regulators , has a DNA-binding site in the N-terminal domain [3] and a signal-recognition site separated in two regions in the amino acid sequence. In the three-dimensional structure of an XapR homolog (CysB from Klebsiella aerogenes), these two regions appear close to each other, forming one signal-binding site. XapR is homologous to AlsR; they show 68% of identity in an amino-terminal region of 60 amino acids [1]. A xapR mutant can not grow on xanthosine [2]. The xapR gene is located downstream of the genes it regulates and in the same direction, but in an independent transcription unit that appears to be expressed constitutively [2]. Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
XapR Non-Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1], [2]
XapR-xanthosine Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1], [2]
Evolutionary Family: LysR
TFBs length: 13
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: xapR
  Genome position: 2521593-2522477
  Length: 885 bp / 294 aa
Operon name: xapR
TU(s) encoding the TF:
Transcription unit        Promoter
xapR
xapRp1
xapR
xapRp2


Regulon       
Regulated gene(s) xapA, xapB
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
nucleotide and nucleoside conversions (1)
carbon compounds (1)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Regulated operon(s) xapAB
First gene in the operon(s) xapA
Simple and complex regulons XapR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[XapR,+](2)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
 LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  XapR-xanthosine activator xapAp Sigma70 -119.0 -151.0 xapA, xapB
ggaattaataTCGCCAATACAGTttttaccgtg
 2525023 2525035 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [2]
  XapR-xanthosine activator xapAp Sigma70 -39.0 -71.0 xapA, xapB
aatgcgtgagAAAAGTGTATTGGtaagagccgg
 2524943 2524955 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [2]
  XapR-xanthosine activator xapAp2 Sigma38 -119.0 -151.0 xapA, xapB
ggaattaataTCGCCAATACAGTttttaccgtg
 2525023 2525035 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [2]
  XapR-xanthosine activator xapAp2 Sigma38 -39.0 -71.0 xapA, xapB
aatgcgtgagAAAAGTGTATTGGtaagagccgg
 2524943 2524955 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [2]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Jorgensen C., Dandanell G., 1999, Isolation and characterization of mutations in the Escherichia coli regulatory protein XapR., J Bacteriol 181(14):4397-403

 [2] Seeger C., Poulsen C., Dandanell G., 1995, Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli., J Bacteriol 177(19):5506-16

 [3] Brun YV., Breton R., Lanouette P., Lapointe J., 1990, Precise mapping and comparison of two evolutionarily related regions of the Escherichia coli K-12 chromosome. Evolution of valU and lysT from an ancestral tRNA operon., J Mol Biol 214(4):825-43


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