5Y61

YfiB-YfiR complexed with GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


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Literature

Structural insights into the functional role of GMP in modulating the YfiBNR system

Zhou, L.Xu, M.Jiang, T.

(2017) Biochem Biophys Res Commun 493: 637-642

  • DOI: 10.1016/j.bbrc.2017.08.139
  • Primary Citation of Related Structures:  
    5Y61, 5Y62

  • PubMed Abstract: 
  • YfiBNR, a tripartite cyclic-di-GMP (c-di-GMP) signalling system, plays an important role in biofilm formation of the gram-negative bacterium P. aeruginosa, which regulates the cellular processes strongly associated with chronic lung infections and drug resistance ...

    YfiBNR, a tripartite cyclic-di-GMP (c-di-GMP) signalling system, plays an important role in biofilm formation of the gram-negative bacterium P. aeruginosa, which regulates the cellular processes strongly associated with chronic lung infections and drug resistance. The outer-membrane lipoprotein YfiB can release the inhibition of the inner membrane protein YfiN by sequestering the periplasmatic protein YfiR, resulting in the activation of diguanylate cyclase activity of YfiN and the production of c-di-GMP. In contrast to the extensive studies on c-di-GMP, little is known about how GMP acts in the YfiBNR system. Here, we report the crystal structures of YfiR complexed with GMP and YfiB L43P -YfiR complexed with GMP. In the YfiR-GMP complex, GMP is located in a hydrophilic pocket formed by R175/H177/R60, while in the YfiB L43P -YfiR-GMP complex, GMP is located in a slightly separated hydrophilic pocket, with GMP forming hydrogen bonds with both YfiB and YfiR. A binding affinity test and biofilm formation assay indicated that GMP may activate diguanylate cyclase activity to promote biofilm production by promoting the affinity of YfiB and YfiR. This finding thus provides a new perspective for preventing biofilm-related antibiotic resistance and chronic infections.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China. Electronic address: tjiang@ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YfiRA, C159Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: yfiRPA1121
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
YfiBB, D138Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: yfiBPA1119
UniProt
Find proteins for Q9I4L6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4L6 
Go to UniProtKB:  Q9I4L6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5GP (Subject of Investigation/LOI)
Query on 5GP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.595α = 107.39
b = 58.422β = 97.28
c = 69.869γ = 89.9
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570768
Strategic Priority Research ProgramChinaXDB08010301

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references