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



Gene: cueR Accession Numbers: G6263 (EcoCyc), b0487, ECK0481

Synonyms: copR, ybbI

Regulation Summary Diagram: ?

Component of:
CueR-Cu(I)
CueR-Cu+ DNA-binding transcriptional dual regulator (extended summary available)

Citations: [Stoyanov01, Outten00, Stoyanov03, Yamamoto05a, Petersen00]

Gene Citations: [Outten00]

Locations: cytosol

Map Position: [513,217 -> 513,624] (11.06 centisomes)
Length: 408 bp / 135 aa

Molecular Weight of Polypeptide: 15.235 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001693 , EchoBASE:EB3044 , EcoGene:EG13256 , EcoliWiki:b0487 , ModBase:P0A9G4 , OU-Microarray:b0487 , PortEco:cueR , PR:PRO_000022348 , Pride:P0A9G4 , Protein Model Portal:P0A9G4 , RefSeq:NP_415020 , RegulonDB:G6263 , SMR:P0A9G4 , String:511145.b0487 , UniProt:P0A9G4

Relationship Links: InterPro:IN-FAMILY:IPR000551 , InterPro:IN-FAMILY:IPR009061 , InterPro:IN-FAMILY:IPR011789 , InterPro:IN-FAMILY:IPR015358 , PDB:Structure:1Q05 , PDB:Structure:1Q06 , PDB:Structure:1Q07 , Pfam:IN-FAMILY:PF00376 , Pfam:IN-FAMILY:PF09278 , Prints:IN-FAMILY:PR00040 , Prosite:IN-FAMILY:PS00552 , Prosite:IN-FAMILY:PS50937 , Smart:IN-FAMILY:SM00422

In Paralogous Gene Group: 141 (4 members)

In Reactions of unknown directionality:

Not in pathways:
CueR + Cu+ = CueR-Cu(I)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Stoyanov01, Petersen00]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
GO:0005507 - copper ion binding Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Essentiality data for cueR 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]

Subunit of: CueR-Cu(I)

Subunit composition of CueR-Cu(I) = [CueR][Cu+]
         CueR transcriptional dual regulator = CueR

Component of: CueR-Cu+ DNA-binding transcriptional dual regulator (extended summary available)

Citations: [Chen03g]

Sequence Length: 135 AAs

In Reactions of unknown directionality:

Not in pathways:
CueR + Cu+ = CueR-Cu(I)

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor


Subunit of: CueR-Cu+ DNA-binding transcriptional dual regulator

Subunit composition of CueR-Cu+ DNA-binding transcriptional dual regulator = [(CueR)(Cu+)]2
         CueR-Cu(I) = (CueR)(Cu+)
                 CueR transcriptional dual regulator = CueR

Summary:
The "Cu efflux regulator", CueR, regulates genes related to the primary copper homeostasis system [Yamamoto05a, Petersen00, Grass01, Outten00] in response to the presence of copper, silver, or gold ions [Yamamoto05a, Stoyanov03a, Stoyanov03].

The crystal structures of CueR dimers bound to Cu+, Ag+, or Au+ have been solved [Changela03]. Each monomer consists of three domains, an N-terminal DNA-binding domain carrying two helix-turn-helix motifs, a central dimerization domain, and a C-terminal metal-binding domain. The DNA-binding and dimerization domains are characteristic of the MerR family of proteins. The dimerization domain contains a 10-turn α-helix that forms an antiparallel coiled-coil with the helix of the other monomer. The metal-binding domain contains an unusual metal receptor site in which the bound metal is inaccessible to the solvent. The metal ion is bound with a linear coordination to two conserved cysteine residues. This dithiolate coordination confers the metal ion selectivity for +1 ions [Changela03]. The sensitivity of CueR for copper(I) ions is extremely high (in the zeptomolar range), which corresponds to less than one atom per cell. Apparently it is the task of CueR and CopA to clear the toxic copper ions rapidly from the cytoplasm into the periplasmic space [Changela03].

CueR activates transcription by overlapping the -35 box of promoters and represses it by binding downstream of the transcription start site [Stoyanov01]. CueR binds to a 19-bp sequence containing two 7-bp inverted repeats separated by a 7-bp spacer [Stoyanov01]. Binding occurs in vitro in both the presence and the absence of copper ions. Holo-CueR binds more strongly to DNA than apo-CueR and with a higher conformational flexibility [Andoy09]. Both holo- and apo-CueR bend DNA [Andoy09]. The formation of permanganate-sensitive transcription complexes requires copper ions [Stoyanov01].

Reviews: [Rensing03, Hobman05, Brown03a, Rademacher12].

Sequence Length: 135 AAs

GO Terms:

Biological Process: GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment [Stoyanov01]
Molecular Function: GO:0044212 - transcription regulatory region DNA binding Inferred from experiment [Stoyanov01]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Credits:
Created 30-May-2008 by Gama-Castro S , UNAM
Last-Curated ? 30-May-2008 by Gama-Castro S , UNAM

DNA binding site length: 19 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: CCTTCCCGTaaCGGGAAGG

Regulated Transcription Units (3 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 69
[UniProt09]
UniProt: HTH merR-type;
DNA-Binding-Region 4 -> 23
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 112
[Stoyanov03, Chen03g, UniProt11]
Alternate sequence: C → S; UniProt: Loss of sensitivity to copper.
Metal-Binding-Site 112
[UniProt10a]
UniProt: Copper(1+);
Mutagenesis-Variant 120
[Stoyanov03, Chen03g, UniProt11]
Alternate sequence: C → S; UniProt: Loss of sensitivity to copper.
Metal-Binding-Site 120
[UniProt10a]
UniProt: Copper(1+);
Mutagenesis-Variant 129
[Stoyanov03, Chen03g, UniProt11]
Alternate sequence: C → S; UniProt: No effect on response to copper.
Mutagenesis-Variant 130
[Stoyanov03, Chen03g, UniProt11]
Alternate sequence: C → S; UniProt: No effect on response to copper.


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

Andoy09: Andoy NM, Sarkar SK, Wang Q, Panda D, Benitez JJ, Kalininskiy A, Chen P (2009). "Single-molecule study of metalloregulator CueR-DNA interactions using engineered Holliday junctions." Biophys J 97(3);844-52. PMID: 19651042

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

Brown03a: Brown NL, Stoyanov JV, Kidd SP, Hobman JL (2003). "The MerR family of transcriptional regulators." FEMS Microbiol Rev 27(2-3);145-63. PMID: 12829265

Changela03: Changela A, Chen K, Xue Y, Holschen J, Outten CE, O'Halloran TV, Mondragon A (2003). "Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR." Science 301(5638);1383-7. PMID: 12958362

Chen03g: Chen K, Yuldasheva S, Penner-Hahn JE, O'Halloran TV (2003). "An atypical linear Cu(I)-S2 center constitutes the high-affinity metal-sensing site in the CueR metalloregulatory protein." J Am Chem Soc 125(40);12088-9. PMID: 14518983

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

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

Grass01: Grass G, Rensing C (2001). "Genes involved in copper homeostasis in Escherichia coli." J Bacteriol 183(6);2145-7. PMID: 11222619

Hobman05: Hobman JL, Wilkie J, Brown NL (2005). "A design for life: prokaryotic metal-binding MerR family regulators." Biometals 18(4);429-36. PMID: 16158235

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

Outten00: Outten FW, Outten CE, Hale J, O'Halloran TV (2000). "Transcriptional activation of an Escherichia coli copper efflux regulon by the chromosomal MerR homologue, cueR." J Biol Chem 275(40);31024-9. PMID: 10915804

Petersen00: Petersen C, Moller LB (2000). "Control of copper homeostasis in Escherichia coli by a P-type ATPase, CopA, and a MerR-like transcriptional activator, CopR." Gene 261(2);289-98. PMID: 11167016

Rademacher12: Rademacher C, Masepohl B (2012). "Copper-responsive gene regulation in bacteria." Microbiology 158(Pt 10);2451-64. PMID: 22918892

Rensing03: Rensing C, Grass G (2003). "Escherichia coli mechanisms of copper homeostasis in a changing environment." FEMS Microbiol Rev 27(2-3);197-213. PMID: 12829268

Stoyanov01: Stoyanov JV, Hobman JL, Brown NL (2001). "CueR (YbbI) of Escherichia coli is a MerR family regulator controlling expression of the copper exporter CopA." Mol Microbiol 39(2);502-11. PMID: 11136469

Stoyanov03: Stoyanov JV, Brown NL (2003). "The Escherichia coli copper-responsive copA promoter is activated by gold." J Biol Chem 278(3);1407-10. PMID: 12446701

Stoyanov03a: Stoyanov JV, Magnani D, Solioz M (2003). "Measurement of cytoplasmic copper, silver, and gold with a lux biosensor shows copper and silver, but not gold, efflux by the CopA ATPase of Escherichia coli." FEBS Lett 546(2-3);391-4. PMID: 12832075

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Yamamoto05a: Yamamoto K, Ishihama A (2005). "Transcriptional response of Escherichia coli to external copper." Mol Microbiol 56(1);215-27. PMID: 15773991


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 Sat Nov 22, 2014, biocyc14.