1JBG,1Q05,1EXI


Conserved Protein Domain Family
HTH_MerR-like

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cd00592: HTH_MerR-like 
Click on image for an interactive view with Cn3D
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators
Helix-turn-helix (HTH) MerR-like transcription regulator, 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: 133378
View PSSM: cd00592
Aligned: 124 rows
Threshold Bit Score: 42.2315
Threshold Setting Gi: 29833868
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA bindingdimer interface
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 YQVKQVAEISGVSIRTLHHYDNIELLnpSALTDa-GYRLYSdADLERLQQILFFKe--IGFRLDEIKEMLDhpnfd---- 75  Bacillus subtilis
1EXI_A        6 YSIGEVSKLANVSIKALRYYDKIDLFkpAYVDPdtSYRYYTdSQLIHLDLIKSLKy--IGTPLEEMKKAQDlemee---- 79  Bacillus subtilis
ZP_01360962   1 MKTMDVCNRLGVTPKGLRVYEEKGLVv-PKRNKn-GYRNYSdIDMLRLREILLLKd--LGFSLQEIKVLLDkniddg--- 73  Clostridium sp. ...
ZP_01370173   1 MQIKEVCEKCKLTKKAIEYYESKNLIh-PQILEn-GYRDYSdADIAVLKEISVLRk--CGVSIADIAEILTssnkpaala 76  Desulfitobacteri...
NP_349065     1 MNTKKVCEKLKISPKALRLYEELNIIv-PNRDEn-NYRNYSeDDLFKLRQVVVLKs--IGIKLKSIKDILDkrkyed--- 73  Clostridium acet...
NP_786075    13 FSTKEVVAITGMTKDALRYYEQQRLIgpVPRNHn-NYRQYSrQNLERLQFVATFRqlgLDLKLLSGDGHIPnraqriqe- 90  Lactobacillus pl...
NP_786416    13 FTTKEVTAMTGMTKDALRYYEHLGILpdVQRNQy-NYRQYShKNLETLQLIKIFRdldLDLSLLTPAHLALdgqa----- 86  Lactobacillus pl...
YP_177004     1 MQIKDFADKYQMQADTIRYYEKQNLLk-PKRREn-GYREYDeECEKQLQLIVVLKq--LGFTIKEIQQLLIlkgkaisae 76  Bacillus clausii...
ZP_01230017   1 MTIKEVEEKTGLTRSNIRFYENENLIk-PLRNErnGYREYSdENVEDIKKIAYLRt--LGITIDDIRNIILqkvs----- 72  Clostridium diff...
YP_252164     1 MQIDEVSKKLNISKSMIRYYEEKGLIn-ISRNQn-NYREFNqTVYTTLKLIKDLKr--LNLSLEEIKYIVNlfnkp---- 72  Staphylococcus h...
Feature 1                                  
1JBG_A       76 ----rkaaLQSQKEILMKKKQRMDEMI 98  Bacillus subtilis
1EXI_A       80 ----lfafYTEQERQIREKLDFLSALE 102 Bacillus subtilis
ZP_01360962  74 --yvfvrsLYFQKQAIQKKIQGLKNIE 98  Clostridium sp. OhILAs
ZP_01370173  77 kckyitelRMQRLNDIQKCMDSLIANY 103 Desulfitobacterium hafniense DCB-2
NP_349065    74 --nkvvniLYMQLKAVENRILELKKIE 98  Clostridium acetobutylicum ATCC 824
NP_786075    91 -lssyratVKKQIAQLQATDQFLAHKI 116 Lactobacillus plantarum WCFS1
NP_786416    87 ----kvvaFKQYQQVIRDRIRHLEAID 109 Lactobacillus plantarum WCFS1
YP_177004    77 cnlsttslLEQKVSDVEEKIQFYQHAL 103 Bacillus clausii KSM-K16
ZP_01230017  73 ----lvevVEKQEKVLETKISDLENAK 95  Clostridium difficile QCD-32g58
YP_252164    73 ---tskecNIQSTKYLDRIIKDYKRSI 96  Staphylococcus haemolyticus JCSC1435

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