6B8A

Crystal structure of MvfR ligand binding domain in complex with M64


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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This is version 1.4 of the entry. See complete history


Literature

Molecular Insights into Function and Competitive Inhibition ofPseudomonas aeruginosaMultiple Virulence Factor Regulator.

Kitao, T.Lepine, F.Babloudi, S.Walte, F.Steinbacher, S.Maskos, K.Blaesse, M.Negri, M.Pucci, M.Zahler, B.Felici, A.Rahme, L.G.

(2018) mBio 9

  • DOI: 10.1128/mBio.02158-17
  • Primary Citation of Related Structures:  
    6B8A

  • PubMed Abstract: 
  • New approaches to antimicrobial drug discovery are urgently needed to combat intractable infections caused by multidrug-resistant (MDR) bacteria. M ultiple v irulence f actor r egulator (MvfR or PqsR), a Pseudomonas aeruginosa quorum sensing transcription factor, regulates functions important in both acute and persistent infections ...

    New approaches to antimicrobial drug discovery are urgently needed to combat intractable infections caused by multidrug-resistant (MDR) bacteria. M ultiple v irulence f actor r egulator (MvfR or PqsR), a Pseudomonas aeruginosa quorum sensing transcription factor, regulates functions important in both acute and persistent infections. Recently identified non-ligand-based benzamine-benzimidazole (BB) inhibitors of MvfR suppress both acute and persistent P. aeruginosa infections in mice without perturbing bacterial growth. Here, we elucidate the crystal structure of the MvfR ligand binding domain (LBD) in complex with one potent BB inhibitor, M64. Structural analysis indicated that M64 binds, like native ligands, to the MvfR hydrophobic cavity. A hydrogen bond and pi interaction were found to be important for MvfR-M64 affinity. Surface plasmon resonance analysis demonstrated that M64 is a competitive inhibitor of MvfR. Moreover, a protein engineering approach revealed that Gln194 and Tyr258 are critical for the interaction between MvfR and M64. Random mutagenesis of the full-length MvfR protein identified a single-amino-acid substitution, I68F, at a DNA binding linker domain that confers M64 insensitivity. In the presence of M64, I68F but not the wild-type (WT) MvfR protein retained DNA binding ability. Our findings strongly suggest that M64 promotes conformational change at the DNA binding domain of MvfR and that the I68F mutation may compensate for this change, indicating allosteric inhibition. This work provides critical new insights into the molecular mechanism of MvfR function and inhibition that could aid in the optimization of anti-MvfR compounds and improve our understanding of MvfR regulation. IMPORTANCE Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that causes serious acute, persistent, and relapsing infections. New approaches to antimicrobial drug discovery are urgently needed to combat intractable infections caused by this pathogen. The Pseudomonas aeruginosa quorum sensing transcription factor MvfR regulates functions important in both acute and persistent infections. We used recently identified inhibitors of MvfR to perform structural studies and reveal important insights that would benefit the optimization of anti-MvfR compounds. Altogether, the results reported here provide critical detailed mechanistic insights into the function of MvfR domains that may benefit the optimization of the chemical, pharmacological, and safety properties of MvfR antagonist series.


    Organizational Affiliation

    Shriners Hospitals for Children Boston, Boston, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding transcriptional regulatorA, B203Pseudomonas aeruginosaMutation(s): 0 
Gene Names: mvfRAO964_20870AOY09_01875B0B20_09895PAERUG_E15_London_28_01_14_10887PAERUG_P32_London_17_VIM_2_10_11_05492PAMH19_4335
UniProt
Find proteins for Q9I4X0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4X0 
Go to UniProtKB:  Q9I4X0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZG (Subject of Investigation/LOI)
Query on CZG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]2-[(5-nitro-1H-benzimidazol-2-yl)sulfanyl]-N-(4-phenoxyphenyl)acetamide
C21 H16 N4 O4 S
IPZUVKDSPDAHMB-UHFFFAOYSA-N
 Ligand Interaction
NCO
Query on NCO

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.556α = 90
b = 121.524β = 90
c = 112.757γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI105902 and AI063433

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.2: 2018-02-28
    Changes: Database references
  • Version 1.3: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence