5H20

X-ray structure of PadR-like Transcription factor from bacteroid fragilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

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This is version 1.2 of the entry. See complete history


Literature

Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis.

Lee, C.Kim, M.I.Hong, M.

(2017) Biochem Biophys Res Commun 483: 264-270

  • DOI: 10.1016/j.bbrc.2016.12.155
  • Primary Citation of Related Structures:  
    5H20

  • PubMed 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 ...

    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.


    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
Putative PadR-family transcriptional regulatory proteinA111Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: BF9343_2549
UniProt
Find proteins for Q5LC36 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow))
Explore Q5LC36 
Go to UniProtKB:  Q5LC36
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.89α = 90
b = 72.89β = 90
c = 84.141γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-13 
  • Released Date: 2017-03-08 
  • Deposition Author(s): Lee, C., Hong, M.

Funding OrganizationLocationGrant Number
National research foundation of koreaKorea, Republic Of2015R1D1A1A01057574

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary