4YN9 | pdb_00004yn9

YfiR mutant-C110S

• PDB DOI: https://doi.org/10.2210/pdb4YN9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-03-09 Released: 2015-04-22 
• Deposition Author(s): Xu, M., Jiang, T.
• Funding Organization(s): the Strategic Priority Research Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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

• PubMed: 25849887 
• DOI: https://doi.org/10.1016/j.bbrc.2015.03.160
• Primary Citation Related Structures: 
  4YN7, 4YN9, 4YNA


• 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 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.

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Organizational Affiliation: 
• 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; 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: [e-mail].
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.95 kDa 
• Atom Count: 2,477 
• Modeled Residue Count: 301 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YfiR	A, B	159	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: yfiR, PA1121
UniProt
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.011	α = 90
b = 121.011	β = 90
c = 86.513	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
the Strategic Priority Research Program	China	XDB08010301

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.3: 2024-10-16
  Changes: Structure summary