Database accession: MF7000668
Name: Transcription factor (Listeria monocytogenes)
PDB ID: 6abq
Experimental method: X-ray (2.30 Å)
Assembly: Homodimer
Source organism: Listeria monocytogenes
Primary publication of the structure:
Lee C, Kim MI, Park J, Hong M
Structure-based molecular characterization and regulatory mechanism of the LftR transcription factor from Listeria monocytogenes: Conformational flexibilities and a ligand-induced regulatory mechanism.
(2019) PLoS ONE 14: e0215017
PMID: 30970033
Abstract:
Listeria monocytogenes is a foodborne pathogen that causes listeriosis and can lead to serious clinical problems, such as sepsis and meningitis, in immunocompromised patients and neonates. Due to a growing number of antibiotic-resistant L. monocytogenes strains, listeriosis can steadily become refractory to antibiotic treatment. To develop novel therapeutics against listeriosis, the drug resistance mechanism of L. monocytogenes needs to be determined. The transcription factor LftR from L. monocytogenes regulates the expression of a putative multidrug resistance transporter, LieAB, and belongs to the PadR-2 subfamily of the PadR family. Despite the functional significance of LftR, our molecular understanding of the transcriptional regulatory mechanism for LftR and even for the PadR-2 subfamily is highly limited. Here, we report the crystal structure of LftR, which forms a dimer and protrudes two winged helix-turn-helix motifs for DNA recognition. Structure-based mutational and comparative analyses showed that LftR interacts with operator DNA through a LftR-specific mode as well as a common mechanism used by the PadR family. Moreover, the LftR dimer harbors one intersubunit cavity in the center of the dimeric structure as a putative ligand-binding site. Finally, conformational flexibilities in the LftR dimer and in the cavity suggest that a ligand-induced regulatory mechanism would be used by the LftR transcription factor.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: PadR family transcriptional regulator
Source organism: Listeria monocytogenes
Length: 108 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKGLTELLKGSLEGMILERISRGETYGYEITKYLNDLGFDEIVEGTVYTILVRLEKKGLVEIEKKKSELGPPRKFYTLSPAGEEELAIFWKRWDFIQGKIMQVKGGQA
UniProtKB AC: L8DXR9 (positions: 1-105)
Coverage: 97%
Name: PadR family transcriptional regulator
Source organism: Listeria monocytogenes
Length: 108 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKGLTELLKGSLEGMILERISRGETYGYEITKYLNDLGFDEIVEGTVYTILVRLEKKGLVEIEKKKSELGPPRKFYTLSPAGEEELAIFWKRWDFIQGKIMQVKGGQA
UniProtKB AC: L8DXR9 (positions: 3-108)
Coverage: 98%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Winged helix DNA-binding domain (PadR family) transcriptional regulator
Evidence level: Direct evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
AphA monomers were found to be highly unstable (PMID:15647287). AphA is a dimer with an N-terminal winged helix DNA-binding domain and a unique C-terminal antiparallel coiled coil domain that serves as its primary dimerization interface and is a case of mutual synergistic folding (MSF). Another PadR family transcriptional regulator, Rv3488, was shown to be a dimer in solution (PMID:30266832), while differential scanning calorimetry-based thermal denaturation data suggested that the PadR family Rv1176c follows two-state unfolding (PMID:38417748).
Chain B:
N/A
Chain A:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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