Conserved Protein Domain Family
HTH_MerD

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cd01111: HTH_MerD 
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator
Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription 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 conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Statistics
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PSSM-Id: 133386
View PSSM: cd01111
Aligned: 8 rows
Threshold Bit Score: 141.755
Threshold Setting Gi: 227575
Created: 30-Apr-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
DNA bindingputative dimer
Feature 1:DNA binding residues [nucleic acid binding site]
Evidence:
  • Comment:Based on sequence similarity to BmrR and the structure of Bacillus subtilis BmrR bound to DNA (1EXI).

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        ###             #                ###                                           
Q52110        4 YTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTgGYGLFDdTALQRLRFVRAAFEAGIGLDALARLCRALDAADgdgASA 83  Acinetobacter ca...
AAF99446     38 LSISQLALAAQTSVHTVRNYVLENLVHCEEKTKsGHSLYGlCALKRLKFIRAARAAGLLVVDIKPLLMAIDAGErkvPED 117 Pseudoalteromona...
AAP88283      4 YTVSRLALNAGVSVHIVRDYLLRGLLRPVACTPgGYGLFDdAALQRLCFVRAAFEAGIGLDALARLCRALDTADgdePAA 83  Delftia acidovorans
1707237A      4 YTVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTgGYGVFDdAALQRLCFVRAAFEAGIGLDALARLCRALDAADgaqAAA 83  Escherichia coli
CAA67453      4 YSISRLAEDAGVSVHIVRDYMLRGLLHPARRTEsGYGIFDeRSLARLCFVRAAFESGIGLDELARLCRALDADDstdVIG 83  Pseudomonas sp.
CAB65707      4 YKISKLAEQAGVSVHVVRDYLLRGLLHPVRRTDsGYGIFDaQSLNRLRFVRTAFEAGIDLRELARWCQSLDGGGg-dIDE 82  Xanthomonas camp...
CAC86908      4 YSISKLAEDAGVTVHVVRDYLMRGLLHPAWRTEgGYNVFDaKTLERLRFLRVAFESGPRHDELTRLCRALDAGDskcVHG 83  Pseudomonas putida
ZP_01110432  23 CVISEAARLCGLSVHQIRTYLDMRLVYACGTTQgGSRLFDdGCLQRLALIRSCREAGLGLPEIAEFIQALDNGDkgqCRA 102 Alteromonas macl...
Feature 1                                  
Q52110       84 QLAVLRQLVERRREALASLEMQLAAMP 110 Acinetobacter calcoaceticus
AAF99446    118 IQKLLLTKIEHRKVFLNLVTNQIEEFC 144 Pseudoalteromonas haloplanktis
AAP88283     84 QLAVLRQFVERRREALADLEVQLATMP 110 Delftia acidovorans
1707237A     84 QLAVVRQLVERRRAALAHLDVQLASMP 110 Escherichia coli
CAA67453     84 CIDRLLGQIATRLAALDAVKTELAGLT 110 Pseudomonas sp.
CAB65707     83 CRAHLRSLIAARRETLVALDRQLAAGL 109 Xanthomonas campestris
CAC86908     84 CVEQLRRKIDVRRKELMVIETSLGELA 110 Pseudomonas putida
ZP_01110432 103 VERQIQHTIAVKRAALNRCTQALTKAA 129 Alteromonas macleodii 'Deep ecotype'

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