The phenylacetic acid regulator , PaaX, is a transcriptional repressor that participates in controlling transcriptional regulation of genes involved in the catabolism of an aromatic compound, phenylacetic acid (PA) . When PaaX is overexpressed, it causes elevated levels of mutations in the genome; therefore, it is a candidate to regulate DNA replication, recombination, or repair .
PaaX contains a helix-turn-helix motif for DNA binding that is similar to the motif found in the N terminal of members of the GntR family of transcriptional regulators . Members of this family share similar N-terminal DNA-binding domains but are classified into four subfamilies according to their divergence in their C-terminal domains, which are involved in effector binding and oligomerization .
Homology with PaaX has been found in other bacteria, such as Pseudomonas putida, Bacillus halodurans, and Arthrobacter sp., among others .
The majority of work concerning PaaX has been done in E.
coli W, in which has been found the DNA-binding sites for PaaX, including a site upstream of the paaXY operon . The DNA-binding consensus of PaaX consists of a palindromic sequence of 6 bp separated by about 27 bp [2, 7]. This palindromic property of the PaaX site as well as the presence of a helix-turn helix motif in the protein have been the basis for suggestions that PaaX binds DNA as a dimer [1, 2].Read more >
The binding of PaaX to DNA is inhibited by phenylacetyl-CoA, which is the product of the first catabolic step in PA degradation [1, 4].
paaX is transcribed in an operon (paaXY) that is located in the genome downstream and in the same orientation as the paaABCDEFGHIJK operon, which is repressed by PaaX .
Crystal structures of the transcriptional repressor PaaX have been determined .
|Sensing class:||Using internal synthesized signals|
|Connectivity class:||Local Regulator|
|Length:||951 bp / 316 aa|
|TU(s) encoding the TF:||
|Regulated gene(s)||paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, paaZ|
|Multifun term(s) of regulated gene(s)||
MultiFun Term (List of genes associated to the multifun term)
carbon compounds (13)
paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaJ, paaK, paaX, paaY, paaZ
Transcription related (1)
|Regulated operon(s)||paaABCDEFGHIJK, paaXY, paaZ|
|First gene in the operon(s)||paaA, paaX, paaZ|
|Simple and complex regulons|
|Simple and complex regulatory phrases||
Regulatory phrase (List of promoters regulated by the phrase)
|Functional conformation||Function||Promoter||Sigma factor||Central Rel-Pos||Distance to first Gene||Genes||Sequence||LeftPos||RightPos||Evidence (Confirmed, Strong, Weak)||References|
|PaaX||repressor||paaAp||Sigma70||30.0||-33.0||paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK||
|1453875||1453913||[BCE], [GEA], [HIBSCS], [SM]||, |
|1453657||1453696||[BCE], [GEA], [HIBSCS], [SM]||, |
|Evolutionary conservation of regulatory elements|
 Kim HS., Kang TS., Hyun JS., Kang HS., 2004, Regulation of penicillin G acylase gene expression in Escherichia coli by repressor PaaX and the cAMP-cAMP receptor protein complex., J Biol Chem. 279(32):33253-62
 Ferrandez A., Minambres B., Garcia B., Olivera ER., Luengo JM., Garcia JL., Diaz E., 1998, Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway., J Biol Chem. 273(40):25974-86
 Rigali S., Derouaux A., Giannotta F., Dusart J., 2002, Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies., J Biol Chem. 277(15):12507-15
 del Peso-Santos T., Bartolome-Martin D., Fernandez C., Alonso S., Garcia JL., Diaz E., Shingler V., Perera J., 2006, Coregulation by phenylacetyl-coenzyme A-responsive PaaX integrates control of the upper and lower pathways for catabolism of styrene by Pseudomonas sp. strain Y2., J Bacteriol. 188(13):4812-21
 Rojas-Altuve A., Carrasco-Lopez C., Hernandez-Rocamora VM., Sanz JM., Hermoso JA., 2011, Crystallization and preliminary X-ray diffraction studies of the transcriptional repressor PaaX, the main regulator of the phenylacetic acid degradation pathway in Escherichia coli W., Acta Crystallogr Sect F Struct Biol Cryst Commun. 67(Pt 10):1278-80