General Information

Database accession: MF7000314

Name: PadR-like transcriptional regulator (Listeria monocytogenes)

PDB ID: 7wjp PDBe

Experimental method: X-ray (2.25 Å)

Assembly: Homodimer

Source organism: Listeria monocytogenes

Primary publication of the structure:

Kim J, Park J, Choi Z, Hong M
Structure-based molecular characterization of the LltR transcription factor from Listeria monocytogenes.

(2022) Biochem. Biophys. Res. Commun. 600: 142-149

PMID: 35219103 PubMed

Abstract:

Listeria monocytogenes is a psychrotrophic food-borne pathogenic bacterium that causes listeriosis. Due to its unusual adaptation, an ability to grow at extended temperatures ranging from 4 to 45 °C, L. monocytogenes is notoriously hard to control in food-manufacturing processes. In addition, the growing number of antibiotic-resistant L. monocytogenes strains have made listeriosis steadily refractory to clinical treatments and can lead to serious life-threatening diseases, such as sepsis and meningitis, in immunocompromised persons and neonates. Transcription factors that belong to the PadR family play a key role in bacterial survival against unfavorable environmental stresses. The LltR protein from L. monocytogenes was identified as a PadR-type transcription factor and was shown to be required for bacterial growth adaptation at low temperatures. Despite the functional significance of LltR in listeria survival and pathogenesis, our molecular understanding of the LltR-mediated transcriptional regulation is highly limited. Here, we report the crystal structure of LltR and reveal the operator DNA recognition mechanism used by LltR. LltR dimerizes into an isosceles triangle-like shape and requires a winged helix-turn-helix motif for dsDNA recognition. Indeed, LltR and putative operator dsDNA binding was observed and suggests a transcriptional repression of the llfR-lmo0600-lmo0601 operon by direct interaction between the LltR transcription factor and its promoter region. Structure-based comparative and mutational analyses showed that LltR interacts with dsDNA via a unique strategy that combines both LltR-specific and PadR family-common mechanisms.


Function and Biology 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

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: A, A-2

Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.

Number of unique protein segments: 1


Chain A

Name: PadR family transcriptional regulator

Source organism: Listeria monocytogenes

Length: 110 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMEVNPQFKKGVLELCCLFLIQKKDCYGYELANQVSKYIEVAEGAIYPVLRRLVKEEYCSTYLVESNEGPSRKYYQLTVKGEIYLNELISEWNNFTDSVAKLLTEGEAVNE

UniProtKB AC: A0A1D2INR9 (positions: 5-105) UniProt

Coverage: 91%

Chain A-2

Name: PadR family transcriptional regulator

Source organism: Listeria monocytogenes

Length: 110 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMEVNPQFKKGVLELCCLFLIQKKDCYGYELANQVSKYIEVAEGAIYPVLRRLVKEEYCSTYLVESNEGPSRKYYQLTVKGEIYLNELISEWNNFTDSVAKLLTEGEAVNE

UniProtKB AC: A0A1D2INR9 (positions: 5-105) UniProt

Coverage: 91%

Evidence 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 A:

N/A

Chain A-2:

N/A

Surface and contacts features:

Related Structure(s) 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).

There are 21 related structures in the MFIB database:
The molecule viewer shows our modified stucture.

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