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: 17-Jan-2013
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:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        ###             #                ###                                           
gi 2498538    4 YTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTgGYGLFDdTALQRLRFVRAAFEAGIGLDALARLCRALDAADgdgASA 83
gi 11496146  38 LSISQLALAAQTSVHTVRNYVLENLVHCEEKTKsGHSLYGlCALKRLKFIRAARAAGLLVVDIKPLLMAIDAGErkvPED 117
gi 32815766   4 YTVSRLALNAGVSVHIVRDYLLRGLLRPVACTPgGYGLFDdAALQRLCFVRAAFEAGIGLDALARLCRALDTADgdePAA 83
gi 227575     4 YTVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTgGYGVFDdAALQRLCFVRAAFEAGIGLDALARLCRALDAADgaqAAA 83
gi 2052184    4 YSISRLAEDAGVSVHIVRDYMLRGLLHPARRTEsGYGIFDeRSLARLCFVRAAFESGIGLDELARLCRALDADDstdVIG 83
gi 6689531    4 YKISKLAEQAGVSVHVVRDYLLRGLLHPVRRTDsGYGIFDaQSLNRLRFVRTAFEAGIDLRELARWCQSLDGGGg-dIDE 82
gi 23821235   4 YSISKLAEDAGVTVHVVRDYLMRGLLHPAWRTEgGYNVFDaKTLERLRFLRVAFESGPRHDELTRLCRALDAGDskcVHG 83
gi 88794727  23 CVISEAARLCGLSVHQIRTYLDMRLVYACGTTQgGSRLFDdGCLQRLALIRSCREAGLGLPEIAEFIQALDNGDkgqCRA 102
                        90       100
                ....*....|....*....|....*..
Feature 1                                  
gi 2498538   84 QLAVLRQLVERRREALASLEMQLAAMP 110
gi 11496146 118 IQKLLLTKIEHRKVFLNLVTNQIEEFC 144
gi 32815766  84 QLAVLRQFVERRREALADLEVQLATMP 110
gi 227575    84 QLAVVRQLVERRRAALAHLDVQLASMP 110
gi 2052184   84 CIDRLLGQIATRLAALDAVKTELAGLT 110
gi 6689531   83 CRAHLRSLIAARRETLVALDRQLAAGL 109
gi 23821235  84 CVEQLRRKIDVRRKELMVIETSLGELA 110
gi 88794727 103 VERQIQHTIAVKRAALNRCTQALTKAA 129

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