3TQN

Structure of the transcriptional regulator of the GntR family, from Coxiella burnetii.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural genomics for drug design against the pathogen Coxiella burnetii.

Franklin, M.C.Cheung, J.Rudolph, M.J.Burshteyn, F.Cassidy, M.Gary, E.Hillerich, B.Yao, Z.K.Carlier, P.R.Totrov, M.Love, J.D.

(2015) Proteins 83: 2124-2136

  • DOI: 10.1002/prot.24841
  • Primary Citation of Related Structures:  
    3UWC, 4NG4, 4F3Q, 4F3R, 3TQH, 3TQI, 3TQJ, 3TQL, 3TQM, 3TQN

  • PubMed Abstract: 
  • Coxiella burnetii is a highly infectious bacterium and potential agent of bioterrorism. However, it has not been studied as extensively as other biological agents, and very few of its proteins have been structurally characterized. To address this sit ...

    Coxiella burnetii is a highly infectious bacterium and potential agent of bioterrorism. However, it has not been studied as extensively as other biological agents, and very few of its proteins have been structurally characterized. To address this situation, we undertook a study of critical metabolic enzymes in C. burnetii that have great potential as drug targets. We used high-throughput techniques to produce novel crystal structures of 48 of these proteins. We selected one protein, C. burnetii dihydrofolate reductase (CbDHFR), for additional work to demonstrate the value of these structures for structure-based drug design. This enzyme's structure reveals a feature in the substrate binding groove that is different between CbDHFR and human dihydrofolate reductase (hDHFR). We then identified a compound by in silico screening that exploits this binding groove difference, and demonstrated that this compound inhibits CbDHFR with at least 25-fold greater potency than hDHFR. Since this binding groove feature is shared by many other prokaryotes, the compound identified could form the basis of a novel antibacterial agent effective against a broad spectrum of pathogenic bacteria.


    Organizational Affiliation

    Special Projects Division, New York Structural Biology Center, New York.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator, GntR familyABC113Coxiella burnetiiMutation(s): 0 
Gene Names: CBU_0775
Find proteins for Q83DG1 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I))
Explore Q83DG1 
Go to UniProtKB:  Q83DG1
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.057α = 90
b = 68.057β = 90
c = 194.466γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2015-07-01
    Changes: Derived calculations
  • Version 1.3: 2015-10-21
    Changes: Database references
  • Version 1.4: 2016-02-10
    Changes: Database references
  • Version 1.5: 2017-11-08
    Changes: Refinement description