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Escherichia coli K-12 substr. MG1655 Polypeptide: PerR transcriptional regulator



Gene: perR Accession Numbers: G6129 (EcoCyc), b0254, ECK0256

Regulation Summary Diagram: ?

Summary:
The PerR transcriptional regulator, which appears to belong to the LysR-family [Bairoch05], has been widely analyzed in B. subtilis, where several DNA binding sites recognized by PerR were identified [Bsat96, Chen95a, Chen95b, Fuangthong02, Herbig01]. In E. coli, the PerR protein and its binding sites has not been analyzed. But an Helix-Turn-Helix motif, that is a characteristic of transcriptional regulators, was observed in the sequence on this protein in E. coli [Bairoch05].

In systematic studies of oligomerization, it was shown that some members of the LysR family, like PerR, interact with other members of the family to form heterodimers, but the physiological significance of this is unknown [Knapp10].

Locations: cytosol

Map Position: [268,513 <- 269,406] (5.79 centisomes)
Length: 894 bp / 297 aa

Molecular Weight of Polypeptide: 33.639 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000862 , DIP:DIP-10463N , EchoBASE:EB3124 , EcoGene:EG13340 , EcoliWiki:b0254 , Mint:MINT-1292741 , ModBase:Q57083 , OU-Microarray:b0254 , PortEco:perR , PR:PRO_000023513 , Pride:Q57083 , Protein Model Portal:Q57083 , RefSeq:NP_414788 , RegulonDB:G6129 , SMR:Q57083 , String:511145.b0254 , UniProt:Q57083

Relationship Links: EcoO157Cyc:Homolog:Z0346 , EcoO157Cyc:Homolog:Z0346-MONOMER , EcoO157Cyc:Homolog:Z0885 , EcoO157Cyc:Homolog:Z0885-MONOMER , InterPro:IN-FAMILY:IPR000847 , InterPro:IN-FAMILY:IPR005119 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF00126 , Pfam:IN-FAMILY:PF03466 , Prints:IN-FAMILY:PR00039 , Prosite:IN-FAMILY:PS50931

In Paralogous Gene Group: 6 (42 members)

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Rajagopala12]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: extrachromosomal prophage genes and phage related functions

Essentiality data for perR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Sequence Features

Feature Class Location Citations Comment
Conserved-Region 7 -> 64
[UniProt09]
UniProt: HTH lysR-type;
DNA-Binding-Region 24 -> 44
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


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

Bairoch05: Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2005). "The Universal Protein Resource (UniProt)." Nucleic Acids Res 33(Database issue);D154-9. PMID: 15608167

Bsat96: Bsat N, Chen L, Helmann JD (1996). "Mutation of the Bacillus subtilis alkyl hydroperoxide reductase (ahpCF) operon reveals compensatory interactions among hydrogen peroxide stress genes." J Bacteriol 178(22);6579-86. PMID: 8932315

Chen95a: Chen L, Helmann JD (1995). "Bacillus subtilis MrgA is a Dps(PexB) homologue: evidence for metalloregulation of an oxidative-stress gene." Mol Microbiol 18(2);295-300. PMID: 8709848

Chen95b: Chen L, Keramati L, Helmann JD (1995). "Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions." Proc Natl Acad Sci U S A 92(18);8190-4. PMID: 7667267

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

Fuangthong02: Fuangthong M, Herbig AF, Bsat N, Helmann JD (2002). "Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible." J Bacteriol 184(12);3276-86. PMID: 12029044

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

Herbig01: Herbig AF, Helmann JD (2001). "Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA." Mol Microbiol 41(4);849-59. PMID: 11532148

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

Knapp10: Knapp GS, Hu JC (2010). "Specificity of the E. coli LysR-type transcriptional regulators." PLoS One 5(12);e15189. PMID: 21187915

PerezRueda04: Perez-Rueda E, Collado-Vides J, Segovia L (2004). "Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea." Comput Biol Chem 28(5-6);341-50. PMID: 15556475

Rajagopala12: Rajagopala SV, Sikorski P, Caufield JH, Tovchigrechko A, Uetz P (2012). "Studying protein complexes by the yeast two-hybrid system." Methods 58(4);392-9. PMID: 22841565

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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


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 Wed Dec 17, 2014, biocyc13.