helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 496663485   432 TPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQQEL 481
Cdd:smart00421   5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQA 54

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496663485 432 TPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQQELLDLVE 486
Cdd:cd06170    2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAI 56

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496663485 427 VESGITPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTqqelldlveaRAALLREA 495
Cdd:COG5905    9 HPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRN----------RVQAVVWA 67

DNA-binding transcriptional regulator, CsgD family [Transcription];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496663485 430 GITPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQQELLDLVEARAAL 491
Cdd:COG2771  127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLGLI 188

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496663485 432 TPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQQELLDLVE 486
Cdd:cd06170    2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAI 56

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 496663485 432 TPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQQELLDLVEA 487
Cdd:COG4566  139 TPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALA 194

two component system response regulator;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 496663485 431 ITPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQQELL 482
Cdd:PRK15369 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201

nitrate/nitrite response regulator protein NarP;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 496663485 431 ITPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQ 478
Cdd:PRK10403 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201

transcriptional regulator UhpA;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 496663485 431 ITPREADTLALLARGRNRKHISEELVVSEETVKSHTSSIYHKLGVHTQQEL 481
Cdd:PRK10360 138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188