Database accession: MF7000661
Name: PadR with p-coumaric acid (Bacillus subtilis)
PDB ID: 5x13
Experimental method: X-ray (1.70 Å)
Assembly: Homodimer
Source organism: Bacillus spizizenii
Primary publication of the structure:
Park SC, Kwak YM, Song WS, Hong M, Yoon SI
Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR.
(2017) Nucleic Acids Res. 45: 13080-13093
PMID: 29136175
Abstract:
The PadR family is a large group of transcriptional regulators that function as environmental sensors. PadR negatively controls the expression of phenolic acid decarboxylase, which detoxifies harmful phenolic acids. To identify the mechanism by which PadR regulates phenolic acid-mediated gene expression, we performed structural and mutational studies of effector and operator recognition by Bacillus subtilis PadR. PadR contains an N-terminal winged helix-turn-helix (wHTH) domain (NTD) and a C-terminal homodimerization domain (CTD) and dimerizes into a dolmen shape. The PadR dimer interacts with the palindromic sequence of the operator DNA using the NTD. Two tyrosine residues and a positively charged residue in the NTD provide major DNA-binding energy and are highly conserved in the PadR family, suggesting that these three residues represent the canonical DNA-binding motif of the PadR family. PadR directly binds a phenolic acid effector molecule using a unique interdomain pocket created between the NTD and the CTD. Although the effector-binding site of PadR is positionally segregated from the DNA-binding site, effector binding to the interdomain pocket causes PadR to be rearranged into a DNA binding-incompatible conformer through an allosteric interdomain-reorganization mechanism.
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, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Transcriptional regulator
Source organism: Bacillus spizizenii
Length: 182 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRVLKYAILGLLRKGELSGYDITSYFKEELGQFWSAKHSQIYPELKKLTDEGFITFRTTIQGTKLEKKMYTLTDSGKQELHDWLIRHQPIPETVKDEFMLKAYFISSLSRQEASDLFTDQLLKRKAKLSDLQGSYEKLMASAEPMSFSSPDFGHYLVLTKALEREKNYVSWLESILAMIDED
UniProtKB AC: E0TW95 (positions: 1-182)
Coverage: 100%
Name: Transcriptional regulator
Source organism: Bacillus spizizenii
Length: 182 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRVLKYAILGLLRKGELSGYDITSYFKEELGQFWSAKHSQIYPELKKLTDEGFITFRTTIQGTKLEKKMYTLTDSGKQELHDWLIRHQPIPETVKDEFMLKAYFISSLSRQEASDLFTDQLLKRKAKLSDLQGSYEKLMASAEPMSFSSPDFGHYLVLTKALEREKNYVSWLESILAMIDED
UniProtKB AC: E0TW95 (positions: 1-182)
Coverage: 100%
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:
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)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
