Database accession: MF7000670
Name: Streptococcus transcriptional regulator
PDB ID: 5zqh
Experimental method: X-ray (2.40 Å)
Assembly: Homodimer
Source organism: Streptococcus pneumoniae
Primary publication of the structure:
Lee C, Kim MI, Park J, Oh H, Kim J, Hong J, Jeon BY, Ka H, Hong M
Structure-based functional analysis of a PadR transcription factor from Streptococcus pneumoniae and characteristic features in the PadR subfamily-2.
(2020) Biochem. Biophys. Res. Commun. 532: 251-257
PMID: 32868077
Abstract:
Since the first discovery of phenolic acid decarboxylase transcriptional regulator (PadR), its homologs have been identified mostly in bacterial species and constitute the PadR family. PadR family members commonly contain a winged helix-turn-helix (wHTH) motif and function as a transcription factor. However, the PadR family members are varied in terms of molecular size and structure. As a result, they are divided into PadR subfamily-1 and PadR subfamily-2. PadR subfamily-2 proteins have been reported in some pathogenic bacteria, including Listeria monocytogenes and Streptococcus pneumoniae, and implicated in drug resistance processes. Despite the growing numbers of known PadR family proteins and their critical functions in bacteria survival, biochemical and biophysical studies of the PadR subfamily-2 are limited. Here, we report the crystal structure of a PadR subfamily-2 member from Streptococcus pneumoniae (SpPadR) at a 2.40 Å resolution. SpPadR forms a dimer using its N-terminal and C-terminal helices. The two wHTH motifs of a SpPadR dimer expose their positively charged residues presumably to interact with DNA. Our structure-based mutational and biochemical study indicates that SpPadR specifically recognizes a palindromic nucleotide sequence upstream of its encoding region as a transcriptional regulator. Furthermore, comparative structural analysis of diverse PadR family members combined with a modeling study highlights the structural and regulatory features of SpPadR that are canonical to the PadR family or specific to the PadR subfamily-2.
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 regulator
Source organism: Streptococcus pneumoniae
Length: 107 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMMKETQLLKGVLEGCVLDMIGQKERYGYELVQTLREAGFDTIVPGTIYPLLQKLEKNQWIRGDMRPSPDGPDRKYFSLMKEGEERVSVFWQQWDDLSQKVEGIKNGG
UniProtKB AC: A0A229FJD3 (positions: 4-105)
Coverage: 95%
Name: PadR family transcriptional regulator
Source organism: Streptococcus pneumoniae
Length: 107 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMMKETQLLKGVLEGCVLDMIGQKERYGYELVQTLREAGFDTIVPGTIYPLLQKLEKNQWIRGDMRPSPDGPDRKYFSLMKEGEERVSVFWQQWDDLSQKVEGIKNGG
UniProtKB AC: A0A229FJD3 (positions: 4-105)
Coverage: 95%
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)
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