Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Protein: PaaX DNA-binding transcriptional repressor



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

Synonyms: ydbY

Regulation Summary Diagram: ?

Component of: PaaX-phenylacetyl-CoA

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

Summary:
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 [Yang04].

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 [Kim04]. The DNA-binding consensus of PaaX consists of a palindromic sequence of 6 bp separated by about 27 bp [Kim04, 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, Kim04].

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)
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: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Ferrandez00]
GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Ferrandez00]
GO:0010124 - phenylacetate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Ferrandez98]
Molecular Function: GO:0000976 - transcription regulatory region sequence-specific DNA binding Inferred from experiment [Ferrandez00]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation type of regulation transcriptional level repressor

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

Symmetry: Inverted Repeat

Regulated Transcription Units (3 total): ?

Notes:

Essentiality data for paaX knockouts: ?

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

Credits:
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 transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 5
[UniProt10a]
Alternate sequence: D → V; UniProt: (in strain: W);
Extrinsic-Sequence-Variant 311
[UniProt10a]
Alternate sequence: L → I; UniProt: (in strain: W);
Extrinsic-Sequence-Variant 315
[UniProt10a]
Alternate sequence: I → T; UniProt: (in strain: W);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

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

GOA01: 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

Kim04: 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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: 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."

Yang04: 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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, biocyc13.