5ZQH

Crystal structure of Streptococcus transcriptional regulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


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Literature

Structure-based functional analysis of a PadR transcription factor from Streptococcus pneumoniae and characteristic features in the PadR subfamily-2.

Lee, C.Kim, M.I.Park, J.Oh, H.Kim, J.Hong, J.Jeon, B.Y.Ka, H.Hong, M.

(2020) Biochem Biophys Res Commun 532: 251-257

  • DOI: 10.1016/j.bbrc.2020.08.035
  • Primary Citation of Related Structures:  
    5ZQH

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea. Electronic address: minsunhong@yonsei.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PadR family transcriptional regulatorA102Streptococcus pneumoniaeMutation(s): 0 
UniProt
Find proteins for A5M9R0 (Streptococcus pneumoniae SP14-BS69)
Explore A5M9R0 
Go to UniProtKB:  A5M9R0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.291 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.301α = 90
b = 30.612β = 127.89
c = 51.481γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-19 
  • Released Date: 2019-05-01 
  • Deposition Author(s): Kim, M., Hong, M.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2015R1D1A1A01057574

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references, Structure summary