4YN7

Non-oxidized YfiR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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:  
    4YNA, 4YN9, 4YN7

  • 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. Electronic address: tjiang@ibp.ac.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YfiRA, B159Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: yfiR, PA1121
Find proteins for Q9I4L4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4L4 
Go to UniProtKB:  Q9I4L4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.725α = 90
b = 120.725β = 90
c = 87.457γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-03-09 
  • Released Date: 2015-04-22 
    • Deposition Author(s): Yang, X., 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
    Changes: Database references