1JBG,1EXI,1Q05


Conserved Protein Domain Family
HTH_MerR-SF

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cd04761: HTH_MerR-SF 
Click on image for an interactive view with Cn3D
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily
Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Statistics
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PSSM-Id: 133389
View PSSM: cd04761
Aligned: 38 rows
Threshold Bit Score: 49.5124
Threshold Setting Gi: 29833868
Created: 19-Dec-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding residues [nucleic acid binding site]
Evidence:
  • Structure:1EXI; Bacillus subtilis BmrR bound to DNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Comment:these residues contact two consecutive major grooves

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1      ###             #                  ###             
1JBG_A      3 YQVKQVAEISGVSIRTLHHYDNIELLn-pSALTDa-GYRLYSdADLERLQQI 52  Bacillus subtilis
1EXI_A      6 YSIGEVSKLANVSIKALRYYDKIDLFk-pAYVDPdtSYRYYTdSQLIHLDLI 56  Bacillus subtilis
1Q05_B      1 MNISDVAKITGLTSKAIRFYEEKGLVt-pPMRSEn-GYRTYTqQHLNELTLL 50  Escherichia coli
AAK48830    1 MKIGELAKATDCAVETIRYYEREQLLp-ePARSDg-NYRLYTqAHVERLTFI 50  Pseudomonas putida
AAD25959    4 LTIGQLAQQTGVSRKAIRLYEEKELIlpsIKRSEg-NYRVYNqEHVFCINGI 54  Bacillus sp. RC607
BAA20105    4 MKIDQVAKRSGLTKRTIRFYEEIGLIp-aPKRTDg-GVRLYSeDDMEELEKV 53  Bacillus subtilis
YP_616043   1 MKIGELSRATGTNIETIRYYERIGLLp-aPARTAg-NYRSYGdAHRARLRFV 50  Sphingopyxis alaskensis RB2256
YP_625525   1 MRIGELAKLSGISASRIRFYEAEGLIt-aVERSAn-GYRDYAdNAVWMLEII 50  Burkholderia cenocepacia AU 1054
AAC33922    8 LTIGVFAKAAGVNVETIRFYQRKGLLr-ePDKPYg-SIRRYGeADVVRVKFV 57  Escherichia coli
CAJ34361    3 FRPADLAHEHGLSPQSVRNYERDGLIp--PARRTesGYRRYTeKHAAALRAY 52  Micromonospora sp. ML1

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