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: 17-Jan-2013
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:
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
Feature 1         ###             #                  ###             
1JBG_A         3 YQVKQVAEISGVSIRTLHHYDNIELLn-pSALTDa-GYRLYSdADLERLQQI 52
1EXI_A         6 YSIGEVSKLANVSIKALRYYDKIDLFk-pAYVDPdtSYRYYTdSQLIHLDLI 56
1Q05_B         1 MNISDVAKITGLTSKAIRFYEEKGLVt-pPMRSEn-GYRTYTqQHLNELTLL 50
gi 13898625    1 MKIGELAKATDCAVETIRYYEREQLLp-ePARSDg-NYRLYTqAHVERLTFI 50
gi 4588029     4 LTIGQLAQQTGVSRKAIRLYEEKELIlpsIKRSEg-NYRVYNqEHVFCINGI 54
gi 2116754     4 MKIDQVAKRSGLTKRTIRFYEEIGLIp-aPKRTDg-GVRLYSeDDMEELEKV 53
gi 103486482   1 MKIGELSRATGTNIETIRYYERIGLLp-aPARTAg-NYRSYGdAHRARLRFV 50
gi 107028430   1 MRIGELAKLSGISASRIRFYEAEGLIt-aVERSAn-GYRDYAdNAVWMLEII 50
gi 3513672     8 LTIGVFAKAAGVNVETIRFYQRKGLLr-ePDKPYg-SIRRYGeADVVRVKFV 57
gi 81681114    3 FRPADLAHEHGLSPQSVRNYERDGLIp--PARRTesGYRRYTeKHAAALRAY 52

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