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Escherichia coli K-12 substr. MG1655 Polypeptide: DhaR DNA-binding transcriptional dual regulator



Gene: dhaR Accession Numbers: G6628 (EcoCyc), b1201, ECK1189

Synonyms: ycgU

Regulation Summary Diagram: ?

Summary:
"Dihydroxyacetone Regulator," DhaR, is negatively autoregulated and coordinately activates transcription of the divergent Dha operon (dhaKLM), which encodes three subunits of the dihydroxyacetone (Dha) kinase [Bachler05].

DhaR is inactivated when DnaK binds to the sensing domain of this regulator, in the absence of Dha [Bachler05]. Dephosphorylated DhaL (DhaL::ADP) is an antagonist of DhaK and also is able to form complexes with the sensing domain of DhaR. In the presence of Dha, DhaL::ADP displaces DhaK or blocks the association of the DhaK/DhaR complex and DhaR activates the transcription of the Dha operon [Bachler05].

DhaR belongs to the family of bacterial enhancer-binding proteins which contain three domains: the sensing domain located in the N terminus, the central AAA+ domain, and the C-terminal domain, which contains a helix-turn-helix motif involved in the interaction with DNA. Although the C-terminal domain and the N-terminal domain from DhaR are similar to those of other members of this group, its central domain is not [Bachler05]. The central AAA+ domain does not contain the two conserved submotives in this family (ESELF and GAFTGA) responsible for interaction with σ54. As with other members of the family, the possibility exists of that this regulator activates dependent promoters of σ70 instead of dependent promoters of σ54 [Bachler05].

The crystal structure has been determined [Shi14a]. DhaR regulates transcription by coiled-coil helix rotation, and this provides the mechanism for transmitting the binding signal from the GAF/PAS domains to the C-terminal DNA-binding domain. [Shi14a].

Locations: cytosol

Map Position: [1,250,289 -> 1,252,208] (26.95 centisomes)
Length: 1920 bp / 639 aa

Molecular Weight of Polypeptide: 70.562 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004033 , DIP:DIP-9438N , EchoBASE:EB3661 , EcoGene:EG13902 , EcoliWiki:b1201 , ModBase:P76016 , OU-Microarray:b1201 , PortEco:dhaR , PR:PRO_000022441 , Pride:P76016 , Protein Model Portal:P76016 , RefSeq:NP_415719 , RegulonDB:G6628 , SMR:P76016 , String:511145.b1201 , UniProt:P76016

Relationship Links: InterPro:IN-FAMILY:IPR000014 , InterPro:IN-FAMILY:IPR002078 , InterPro:IN-FAMILY:IPR002197 , InterPro:IN-FAMILY:IPR003018 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR013767 , InterPro:IN-FAMILY:IPR025662 , InterPro:IN-FAMILY:IPR025943 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00158 , Pfam:IN-FAMILY:PF00989 , Pfam:IN-FAMILY:PF01590 , Pfam:IN-FAMILY:PF02954 , Prosite:IN-FAMILY:PS00675 , Prosite:IN-FAMILY:PS00676 , Prosite:IN-FAMILY:PS00688 , Prosite:IN-FAMILY:PS50045 , Prosite:IN-FAMILY:PS50112 , Smart:IN-FAMILY:SM00065 , Smart:IN-FAMILY:SM00091 , Smart:IN-FAMILY:SM00382

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Bachler05]
GO:0006071 - glycerol metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008134 - transcription factor binding Inferred by computational analysis [GOA01]
GO:0043565 - sequence-specific DNA binding Inferred by computational analysis [GOA01]
Cellular Component: 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 complex regulation two component regulatory systems (external signal)
regulation type of regulation transcriptional level repressor

Symmetry: Inverted Repeat

Regulated Transcription Units (2 total): ?

Notes:

Essentiality data for dhaR 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]

Credits:
Last-Curated ? 12-Jan-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 1 -> 318
[UniProt10]
UniProt: Sensor domain; Sequence Annotation Type: region of interest;
Conserved-Region 52 -> 189
[UniProt09]
UniProt: GAF;
Conserved-Region 201 -> 271
[UniProt09]
UniProt: PAS;
Conserved-Region 319 -> 543
[UniProt09]
UniProt: Sigma-54 factor interaction;
Nucleotide-Phosphate-Binding-Region 355 -> 362
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: potential;
Nucleotide-Phosphate-Binding-Region 415 -> 424
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: potential;
DNA-Binding-Region 608 -> 626
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
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

Bachler05: Bachler C, Schneider P, Bahler P, Lustig A, Erni B (2005). "Escherichia coli dihydroxyacetone kinase controls gene expression by binding to transcription factor DhaR." EMBO J 24(2);283-93. PMID: 15616579

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

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

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

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Shi14a: Shi R, McDonald L, Cygler M, Ekiel I (2014). "Coiled-coil helix rotation selects repressing or activating state of transcriptional regulator DhaR." Structure 22(3);478-87. PMID: 24440518

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.

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

Other References Related to Gene Regulation

GamaCastro08: Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J (2008). "RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation." Nucleic Acids Res 36(Database issue);D120-4. PMID: 18158297


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 Sun Nov 23, 2014, biocyc14.