4YNA

Oxidized YfiR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of YfiR from Pseudomonas aeruginosa in two redox states

Yang, X.Yang, X.-A.Xu, M.Zhou, L.Fan, Z.Jiang, T.

(2015) Biochem.Biophys.Res.Commun. 461: 14-20

  • DOI: 10.1016/j.bbrc.2015.03.160
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • YfiBNR is a recently identified c-di-GMP regulatory system involved in bacterial biofilm formation. The periplasmic protein YfiR inhibits the diguanylate cyclase activity of the inner membrane protein YfiN, whereas YfiB in the outer membrane can rele ...

    YfiBNR is a recently identified c-di-GMP regulatory system involved in bacterial biofilm formation. The periplasmic protein YfiR inhibits the diguanylate cyclase activity of the inner membrane protein YfiN, whereas YfiB in the outer membrane can release this inhibition by sequestration of YfiR. In addition, this system may respond to anoxic conditions via YfiR, although the detailed mechanism is still unknown. Here we report crystal structures of Pseudomonas aeruginosa YfiR in the absence and presence of oxidative glutathione. Our structures reveal the overall folding of YfiR for the first time and demonstrate that YfiR exist as a dimer. Comparison of the two structures in different redox states revealed a broken/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152). Mutagenesis studies indicated that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.,Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China. Electronic address: fanz@moon.ibp.ac.cn.,Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China. Electronic address: tjiang@ibp.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YfiR
A, B, C, D
159Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: yfiR
Find proteins for Q9I4L4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I4L4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.246 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 119.668α = 90.00
b = 119.668β = 90.00
c = 85.776γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-03-09 
  • Released Date: 2015-04-22 
  • Deposition Author(s): Xu, M., Jiang, T.

Funding OrganizationLocationGrant Number
the Strategic Priority Research ProgramChinaXDB08010301

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-20
    Type: Database references