Conserved Protein Domain Family
LuxR_C_like

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cd06170: LuxR_C_like 
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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.
Statistics
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PSSM-Id: 99777
View PSSM: cd06170
Aligned: 65 rows
Threshold Bit Score: 47.5292
Threshold Setting Gi: 24158735
Created: 8-Jan-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA bindingdimerization
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding residues [nucleic acid binding site]
Evidence:
  • Comment:based on the binding of A.tumefaciens TraR, M.tuberculosis DosR, and E.coli NarL to their target binding sites. Many of these LuxR_like proteins are active as dimers, and may share a similar organization of these target binding sites.
  • Structure:1ZLK, Mycobacterium tuberculosis DosR C-terminal domain dimer, bound with DNA, contacts at 3.5A.
    View structure with Cn3D
  • Structure:1H0M, Agrobacterium tumefaciens TraR dimer bound to target DNA, contacts at 3.5 A.
    View structure with Cn3D
  • Structure:1JE8, Escherichia coli NarL dimer, bound with a 20-nucleotide DNA containing a palindromic tail-to-tail arrangement of the nirB -74 promotor site, contacts at 3.5A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
Feature 1        ###            ###       ## ## #####          #         
1FSE_B       12 LTKREREVFELLVqDKTTKEIASELFISEKTVRNHISNAMQKLGvkgRSQAVVELLR 68
1ZLK_A       28 LTDQERTLLGLLSeGLTNKQIADRMFLAEKTVKNYVSRLLAKLGmerRTQAAVFATE 84
1P4W_A       35 LSPKESEVLRLFAeGFLVTEIAKKLNRSIKTISSQKKSAMMKLGvdnDIALLNYLSS 91
gi 60393000 138 LSRTESSMLRMWMaGQGTIQISDQMNIKAKTVSSHKGNIKRKIKthnKQVIYHVVRL 194
gi 464931    19 LTDKEFETLVLYCqMMNVQMVADYQNRKPDVIIKHLKSCRQKIGvesDFELYFIVIN 75
gi 3915634  103 LSPTEREILRFMSrGYSMTQIAEQLKRNIKTIRAHKFNVMSKLGvssDAGLLEAADI 159
gi 83288197 154 LTLSERKVLRLLGkGWGINQIASLLKKSNKTISAQKNSAMRRLAihsNAEMYAWINS 210
gi 2506596   25 VSEKERLLLKLLMqGMSVTEISQYRNRSAKTISHQKKQLFEKLGiqsDITFWRDIFF 81
gi 6015049  140 LTPQEEKVLSMWMdGVSNNAIAAALSIHGKTVYTYKRNIRMKLHlgnRFSPFLSLPG 196
gi 9297035  184 LSRRELQCLEMTAnGLLAKQICARLSISVSAVQLYLASARRKLTvatTSEQLLGPRR 240

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