3TRF

Structure of a shikimate kinase (aroK) from Coxiella burnetii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1002/prot.24841
  • Primary Citation of Related Structures:  
    3TQ8, 3TQ9, 3TQA, 3TQB, 3TQC, 3TQD, 3TQE, 3TQF, 3TQG, 3TQH, 3TQI, 3TQJ, 3TQL, 3TQM, 3TQN, 3TQO, 3TQP, 3TQQ, 3TQR, 3TQS, 3TQT, 3TQU, 3TQW, 3TQX, 3TQY, 3TQZ, 3TR0, 3TR1, 3TR2, 3TR3, 3TR4, 3TR5, 3TR6, 3TR7, 3TR8, 3TR9, 3TRB, 3TRC, 3TRD, 3TRE, 3TRF, 3TRG, 3TRH, 3TRI, 3TTH, 3TY2, 3UWC, 4F3Q, 4F3R, 4NBQ

  • 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Shikimate kinase
A, B
185Coxiella burnetiiMutation(s): 0 
Gene Names: aroKCBU_1892
EC: 2.7.1.71
UniProt
Find proteins for Q83AJ3 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I))
Explore Q83AJ3 
Go to UniProtKB:  Q83AJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83AJ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.429α = 90
b = 98.429β = 90
c = 157.071γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description