Escherichia coli K-12 substr. MG1655 Protein: PaaX DNA-binding transcriptional repressor
Inferred by computational analysisInferred from experiment

Gene: paaX Accession Numbers: G6720 (EcoCyc), b1399, ECK1396

Synonyms: ydbY

Regulation Summary Diagram

Regulation summary diagram for paaX

Component of: PaaX-phenylacetyl-CoA

Subunit composition of PaaX DNA-binding transcriptional repressor = [PaaX]2

The "phenylacetic acid" regulator [Ferrandez98], PaaX, is a transcriptional repressor that participates in controlling transcriptional regulation of genes involved in the catabolism of an aromatic compound, phenylacetic acid (PA) [Ferrandez00]. 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 [Yang04c].

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 [Ferrandez98]. 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 [Rigali02].

Homology with PaaX has been found in other bacteria, such as Pseudomonas putida, Bacillus halodurans, and Arthrobacter sp., among others [Ferrandez00].

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 [Kim04e]. The DNA-binding consensus of PaaX consists of a palindromic sequence of 6 bp separated by about 27 bp [Kim04e, delPesoSantos06]. 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 [Ferrandez00, Kim04e].

The binding of PaaX to DNA is inhibited by phenylacetyl-CoA, which is the product of the first catabolic step in PA degradation [Ferrandez00, Ferrandez98].

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 [Ferrandez00].

Crystal structures of the transcriptional repressor PaaX have been determined [RojasAltuve11].

Citations: [Leonhartsberger01]

Gene Citations: [Fernandez14]

Locations: cytosol

Map Position: [1,461,563 -> 1,462,513] (31.5 centisomes, 113°)
Length: 951 bp / 316 aa

Molecular Weight of Polypeptide: 35.295 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004674, DIP:DIP-10431N, EchoBASE:EB3509, EcoGene:EG13746, EcoliWiki:b1399, OU-Microarray:b1399, PortEco:paaX, PR:PRO_000023482, Protein Model Portal:P76086, RefSeq:NP_415917, RegulonDB:G6720, SMR:P76086, String:511145.b1399, UniProt:P76086

Relationship Links: InterPro:IN-FAMILY:IPR011965, InterPro:IN-FAMILY:IPR012906, InterPro:IN-FAMILY:IPR013225, Pfam:IN-FAMILY:PF07848, Pfam:IN-FAMILY:PF08223

In Reactions of unknown directionality:

Not in pathways:
PaaX + phenylacetyl-CoA = PaaX-phenylacetyl-CoA

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for paaX

GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0006351 - transcription, DNA-templated [UniProtGOA11a, GOA01a, Ferrandez00]
Inferred from experimentInferred by computational analysisGO:0010124 - phenylacetate catabolic process [UniProtGOA12, Ferrandez98]
Inferred from experimentGO:2000143 - negative regulation of DNA-templated transcription, initiation [Ferrandez00]
Inferred by computational analysisGO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0000984 - bacterial-type RNA polymerase regulatory region sequence-specific DNA binding [Ferrandez00]
Inferred from experimentGO:0005515 - protein binding [Rajagopala14]
Inferred by computational analysisGO:0003677 - DNA binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: information transferRNA relatedTranscription related
metabolismcarbon utilizationcarbon compounds
regulationtype of regulationtranscriptional levelrepressor

DNA binding site length: 15 base-pairs, 39 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (3 total):


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for paaX knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Created 09-Oct-2008 by Gama-Castro S, UNAM
Last-Curated 10-Oct-2008 by Gama-Castro S, UNAM

Subunit of: PaaX-phenylacetyl-CoA

Subunit composition of PaaX-phenylacetyl-CoA = [PaaX][phenylacetyl-CoA]

Citations: [Ferrandez00]

Sequence Length: 316 AAs

In Reactions of unknown directionality:

Not in pathways:
PaaX + phenylacetyl-CoA = PaaX-phenylacetyl-CoA

MultiFun Terms: information transferRNA relatedTranscription related
metabolismcarbon utilizationcarbon compounds
regulationtype of regulationtranscriptional levelrepressor

Sequence Features

Protein sequence of PaaX with features indicated

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 5
Author statement[UniProt15]
UniProt: In strain: W..
Pfam PF07848 19 -> 87
Inferred by computational analysis[Finn14]
PaaX : PaaX-like protein
Pfam PF08223 104 -> 273
Inferred by computational analysis[Finn14]
PaaX_C : PaaX-like protein C-terminal domain
Extrinsic-Sequence-Variant 311
Author statement[UniProt15]
UniProt: In strain: W..
Extrinsic-Sequence-Variant 315
Author statement[UniProt15]
UniProt: In strain: W..

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

delPesoSantos06: 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. PMID: 16788190

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Fernandez14: Fernandez C, Diaz E, Garcia JL (2014). "Insights on the regulation of the phenylacetate degradation pathway from Escherichia coli." Environ Microbiol Rep 6(3);239-50. PMID: 24983528

Ferrandez00: Ferrandez A, Garcia JL, Diaz E (2000). "Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli." J Biol Chem 275(16);12214-22. PMID: 10766858

Ferrandez98: 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 1998;273(40);25974-86. PMID: 9748275

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kim04e: 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. PMID: 15159386

Leonhartsberger01: Leonhartsberger S, Huber A, Lottspeich F, Bock A (2001). "The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system." J Mol Biol 2001;307(1);93-105. PMID: 11243806

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Rigali02: 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. PMID: 11756427

RojasAltuve11: 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. PMID: 22102047

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Yang04c: Yang H, Wolff E, Kim M, Diep A, Miller JH (2004). "Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach." Mol Microbiol 53(1);283-95. PMID: 15225322

Other References Related to Gene Regulation

Kaleta10: Kaleta C, Gohler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010). "Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis." BMC Syst Biol 4;116. PMID: 20718955

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by Pathway Tools version 19.5 (software by SRI International) on Wed Nov 25, 2015, biocyc14.