8G8V

GTP Cyclohydrolase-IB with sodium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Combatting melioidosis with chemical synthetic lethality.

Zhang, Y.McWhorter, K.L.Rosen, P.C.Klaus, J.R.Gallant, E.Amaya Lopez, C.Y.Jhunjhunwala, R.Chandler, J.R.Davis, K.M.Seyedsayamdost, M.R.

(2024) Proc Natl Acad Sci U S A 121: e2406771121-e2406771121

  • DOI: https://doi.org/10.1073/pnas.2406771121
  • Primary Citation of Related Structures:  
    8G6C, 8G8V, 8TCC

  • PubMed Abstract: 

    Burkholderia thailandensis has emerged as a nonpathogenic surrogate for Burkholderia pseudomallei , the causative agent of melioidosis, and an important Gram-negative model bacterium for studying the biosynthesis and regulation of secondary metabolism. We recently reported that subinhibitory concentrations of trimethoprim induce vast changes in both the primary and secondary metabolome of B. thailandensis . In the current work, we show that the folate biosynthetic enzyme FolE2 is permissive under standard growth conditions but essential for B. thailandensis in the presence of subinhibitory doses of trimethoprim. Reasoning that FolE2 may serve as an attractive drug target, we screened for and identified ten inhibitors, including dehydrocostus lactone (DHL), parthenolide, and β-lapachone, all of which are innocuous individually but form a chemical-synthetic lethal combination with subinhibitory doses of trimethoprim. We show that DHL is a mechanism-based inhibitor of FolE2 and capture the structure of the covalently inhibited enzyme using X-ray crystallography. In vitro, the combination of subinhibitory trimethoprim and DHL is more potent than Bactrim, the current standard of care against melioidosis. Moreover, unlike Bactrim, this combination does not affect the growth of most commensal and beneficial gut bacteria tested, thereby providing a degree of specificity against B. pseudomallei . Our work provides a path for identifying antimicrobial drug targets and for utilizing binary combinations of molecules that form a toxic cocktail based on metabolic idiosyncrasies of specific pathogens.


  • Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ 08544.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP cyclohydrolase FolE2
A, B
303Burkholderia pseudomalleiMutation(s): 0 
Gene Names: folE2BURPS406E_D0599
EC: 3.5.4.16
UniProt
Find proteins for Q63JF5 (Burkholderia pseudomallei (strain K96243))
Explore Q63JF5 
Go to UniProtKB:  Q63JF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63JF5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A],
S [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
M [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO3
Query on SO3

Download Ideal Coordinates CCD File 
D [auth A],
H [auth A],
L [auth B],
P [auth B],
Q [auth B]
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth A]
J [auth A]
N [auth B]
F [auth A],
G [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
SNC
Query on SNC
A, B
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.499α = 90
b = 116.499β = 90
c = 70.806γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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 StatesR35-GM147557

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2024-11-20
    Changes: Database references