Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.65 kDa 
• Atom Count: 4559 
• Residue Count: 591 
• Unique protein chains: 1

4JIT

Crystal Structure of E. coli XGPRT in complex with (S)-3-(Guanin-9-yl)pyrrolidin-N-ylacetylphosphonic acid

• DOI: 10.2210/pdb4JIT/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli str. K-12 substr. MDS42
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-07 Released: 2014-12-24 
• Deposition Author(s): Keough, D.T., Hockova, D., Rejman, D., Spacek, P., Vrbkova, S., Krecmerova, M., Eng, W.S., Jans, H., West, N.P., Naesens, L.M.J., de Jersey, J., Guddat, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 
• R-Value Observed: 0.213 

Literature

Inhibition of the Escherichia coli 6-oxopurine phosphoribosyltransferases by nucleoside phosphonates: potential for new antibacterial agents.

Keough, D.T., Hockova, D., Rejman, D., Spacek, P., Vrbkova, S., Krecmerova, M., Eng, W.S., Jans, H., West, N.P., Naesens, L.M., de Jersey, J., Guddat, L.W.

(2013) J Med Chem 56: 6967-6984

• PubMed: 23927482 
• DOI: 10.1021/jm400779n
• Primary Citation of Related Structures:  
  4JIT, 4JLS


• PubMed Abstract: 
  

Escherichia coli (Ec) cells possess two purine salvage enzymes: xanthine-guanine phosphoribosyltransferase (XGPRT) and hypoxanthine phosphoribosyltransferase (HPRT). EcXGPRT shares a common structural feature with other members of this family, a flexible loop that closes over the active site during catalysis. The replacement of six of these amino acids by alanine has no effect on the Km for the two substrates. However, the Ki for the nucleoside monophosphate increases by 27-fold, and the kcat is reduced by ∼200-fold. Nucleoside phosphonates (NP) are good inhibitors of EcXGPRT and EcHPRT, with Ki values as low as 10 nM. In the absence of the flexible loop, these values increase by 5- to 30-fold, indicating the importance of the loop for high-affinity inhibition. Crystal structures of two NPs in complex with EcXGPRT explain the tight binding. Prodrugs of NPs with low Ki values for EcXGPRT or EcHPRT exhibit IC50 values between 5 and 23 μM against Mycobacterium tuberculosis in cell-based assays, suggesting that these compounds are therapeutic leads against pathogenic bacteria.

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Organizational Affiliation: 

The School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane, 4072 QLD, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthine phosphoribosyltransferase	A, B, C, D	152	Escherichia coli str. K-12 substr. MDS42	Mutation(s): 0  Gene Names: gpt, ECMDS42_0227 EC: 2.4.2.22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3ZF	B, C	{2-[(3S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)pyrrolidin-1-yl]-2-oxoethyl}phosphonic acid C11 H15 N6 O5 P DPSMTUGMQGDYNX-LURJTMIESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 
• R-Value Observed: 0.213 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.066	α = 90
b = 94.066	β = 90
c = 162.633	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-07 
• Released Date: 2014-12-24 
Deposition Author(s): Keough, D.T., Hockova, D., Rejman, D., Spacek, P., Vrbkova, S., Krecmerova, M., Eng, W.S., Jans, H., West, N.P., Naesens, L.M.J., de Jersey, J., Guddat, L.W.

Revision History 

• Version 1.0: 2014-12-24
  Type: Initial release