6UGL

VqmA bound to DPO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism underlying autoinducer recognition in theVibrio choleraeDPO-VqmA quorum-sensing pathway.

Huang, X.Duddy, O.P.Silpe, J.E.Paczkowski, J.E.Cong, J.Henke, B.R.Bassler, B.L.

(2020) J Biol Chem 295: 2916-2931

  • DOI: https://doi.org/10.1074/jbc.RA119.012104
  • Primary Citation of Related Structures:  
    6UGL

  • PubMed Abstract: 

    Quorum sensing is a bacterial communication process whereby bacteria produce, release, and detect extracellular signaling molecules called autoinducers to coordinate collective behaviors. In the pathogen Vibrio cholerae , the quorum-sensing autoinducer 3,5-dimethyl-pyrazin-2-ol (DPO) binds the receptor and transcription factor VqmA. The DPO-VqmA complex activates transcription of vqmR , encoding the VqmR small RNA, which represses genes required for biofilm formation and virulence factor production. Here, we show that VqmA is soluble and properly folded and activates basal-level transcription of its target vqmR in the absence of DPO. VqmA transcriptional activity is increased in response to increasing concentrations of DPO, allowing VqmA to drive the V. cholerae quorum-sensing transition at high cell densities. We solved the DPO-VqmA crystal structure to 2.0 Å resolution and compared it with existing structures to understand the conformational changes VqmA undergoes upon DNA binding. Analysis of DPO analogs showed that a hydroxyl or carbonyl group at the 2'-position is critical for binding to VqmA. The proposed DPO precursor, a linear molecule, N -alanyl-aminoacetone (Ala-AA), also bound and activated VqmA. Results from site-directed mutagenesis and competitive ligand-binding analyses revealed that DPO and Ala-AA occupy the same binding site. In summary, our structure-function analysis identifies key features required for VqmA activation and DNA binding and establishes that, whereas VqmA binds two different ligands, VqmA does not require a bound ligand for folding or basal transcriptional activity. However, bound ligand is required for maximal activity.


  • Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Helix-turn-helix transcriptional regulator
A, B
246Vibrio cholerae O1 str. 2010EL-1786Mutation(s): 0 
Gene Names: C9J66_03310EC575_07960EN12_18880ERS013215_03763EYB64_07770
UniProt
Find proteins for A0A0F0AZW0 (Vibrio cholerae)
Explore A0A0F0AZW0 
Go to UniProtKB:  A0A0F0AZW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F0AZW0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.280 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.459α = 90
b = 84.68β = 90
c = 116.042γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R37GM065859
National Science Foundation (NSF, United States)United StatesMCB-1713731
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Advisory, Data collection, Database references