1EFA,1BDH,2BJC,1UXC,1QPZ,1JFT,1PNR,1JFS,2PUG,2PUE,2PUD,2PUA,1JH9,1RZR,1ZVV,1VPW,1CJG,2PE5,1L1M


Conserved Protein Domain Family
HTH_LacI

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cd01392: HTH_LacI 
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Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators
HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.
Statistics
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PSSM-Id: 143331
View PSSM: cd01392
Aligned: 1351 rows
Threshold Bit Score: 41.2397
Threshold Setting Gi: 91786254
Created: 12-Dec-2003
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA bindingdomain linker
Conserved site includes 18 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding site [nucleic acid binding site]
Evidence:
  • Structure:1EFA_A; Escherichia coli LacI binds the operator DNA; contacts at 3.5A
    View structure with Cn3D
  • Structure:1PNR_A; Escherichia coli PurR binds the operator DNA; contacts at 3.5A
    View structure with Cn3D
  • Citation:PMID 7973627
  • Structure:1RZR_G; Bacillus megaterium CcpA (transcription regulator) binds DNA; contacts at 3.5A
    View structure with Cn3D
  • Comment:The DNA-binding domain of LacI family contains a HTH motif that makes base-specific contacts in the major groove of the operator DNA

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1       #       ##### ##  #    ##  #            #  #  ## ## 
1EFA_A        7 YDVAEYAGVSYQTVSRVVNQashVSAKTREKVEAAMAELNYIPNRVAQQLAG 58  Escherichia coli
BAB06032      4 SDVAKLANVSPATVSRVLSNpelVSKETRKKVLDVINQVNYKPHIVARQFRT 55  Bacillus halodurans C-125
ZP_02925020   9 EDVARAAGVSVATVSRALKDdsrISPTVREAVKAVAVRMGYVPNPLVQSLMS 60  Verrucomicrobium spinosum DSM 4136
YP_525982     5 REVARVAGVSVATVSRALSHpekVSPASMKKVKQAIEEVNYRPNMLARNFRS 56  Saccharophagus degradans 2-40
NP_356282    10 REVAALAGVSIATVSRALQQpdkVRPETRKKVFDAVRQANFVPNAQAASFRR 61  Agrobacterium tumefaciens str. C58
ABA21790     34 EDIARKAGVSHSTVSRALRDsplISSQVREDIKKLAQEMNYVPNAIAKSLQT 85  Anabaena variabilis ATCC 29413
ABE58125      5 RKVAELAGVSVATVSRALKTpdvVSPGTRDKVLAAVEQADYRPNLTAVQFRS 56  Chromohalobacter salexigens DSM 3043
AAO78718     10 KDLAQALGVSIPTVSRALKDspeISRELCAKAKKLAKEMNYRPNPFAMSLRK 61  Bacteroides thetaiotaomicron VPI-5482
ZP_02849123   9 KDLAVKAGLSVNTISRALKDkedIAASTRQMIKDLAKEMGYVGNALAGSLRS 60  Paenibacillus sp. JDR-2
ZP_03458662  10 SDIAAIAGVSSGTVDRILHNrggVSPESRKKVEDVLQQINYVCKIHSITPKN 61  Bacteroides eggerthii DSM 20697

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