Database accession: MF7000315
Name: PadR-like transcriptional regulator (Bacteroides fragilis NCTC 9343)
PDB ID: 5h20
Experimental method: X-ray (2.50 Å)
Assembly: Homodimer
Source organism: Bacteroides fragilis
Primary publication of the structure:
Lee C, Kim MI, Hong M
Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis.
(2017) Biochem. Biophys. Res. Commun. 483: 264-270
PMID: 28027933
Abstract:
A phenolic acid decarboxylase (padC) regulator, PadR and its homologs proteins belong to the PadR family. Despite the growing numbers of the PadR family members and their various roles in bacteria, such as detoxifications, drug transports and circadian rhythms, biochemical and biophysical studies of the PadR family are very limited. Thus, a ligand-induced regulatory mechanism of the PadR family transcription factors remains to be elucidated. Here, we report a crystal structure of a Bacteroides fragilis PadR-like protein, BF2549 and revealed its interaction with putative operator DNA and ligand molecules. Comparative structural and primary sequence analyses provide a PadR-specific motif that is conserved in the PadR family but deviated from the MarR family. Furthermore, putative ligand binding sites are observed in the BF2549 structure. Finally, a homology-based structure model of BF2549 and 29-mer dsDNA propose regulatory mechanisms of the PadR family in transcriptional derepression.
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: PadR-family transcriptional regulatory protein
Source organism: Bacteroides fragilis
Length: 111 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNVDNVKSQMRKGMLEYCIMLLLHKEPAYASDIIQKLKEARLIVVEGTLYPLLTRLKNDDLLSYEWVESTQGPPRKYYKLTGKGESFLGELEASWKELNETVNHIANRESI
UniProtKB AC: Q5LC36 (positions: 4-106)
Coverage: 92%
Name: PadR-family transcriptional regulatory protein
Source organism: Bacteroides fragilis
Length: 111 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNVDNVKSQMRKGMLEYCIMLLLHKEPAYASDIIQKLKEARLIVVEGTLYPLLTRLKNDDLLSYEWVESTQGPPRKYYKLTGKGESFLGELEASWKELNETVNHIANRESI
UniProtKB AC: Q5LC36 (positions: 4-106)
Coverage: 92%
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)
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