7KL7

Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase-A Putative Target for Drug Discovery against Gastrointestinal Tract Infections.

Keough, D.T.Wun, S.J.Baszczynski, O.Eng, W.S.Spacek, P.Panjikar, S.Naesens, L.Pohl, R.Rejman, D.Hockova, D.Ferrero, R.L.Guddat, L.W.

(2021) J Med Chem 64: 5710-5729

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02184
  • Primary Citation of Related Structures:  
    7KL6, 7KL7

  • PubMed Abstract: 

    Helicobacter pylori (Hp) is a human pathogen that lives in the gastric mucosa of approximately 50% of the world's population causing gastritis, peptic ulcers, and gastric cancer. An increase in resistance to current drugs has sparked the search for new Hp drug targets and therapeutics. One target is the disruption of nucleic acid production, which can be achieved by impeding the synthesis of 6-oxopurine nucleoside monophosphates, the precursors of DNA and RNA. These metabolites are synthesized by Hp xanthine-guanine-hypoxanthine phosphoribosyltransferase (XGHPRT). Here, nucleoside phosphonates have been evaluated, which inhibit the activity of this enzyme with K i values as low as 200 nM. The prodrugs of these compounds arrest the growth of Hp at a concentration of 50 μM in cell-based assays. The kinetic properties of HpXGHPRT have been determined together with its X-ray crystal structure in the absence and presence of 9-[( N -3-phosphonopropyl)-aminomethyl-9-deazahypoxanthine, providing a basis for new antibiotic development.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribosyltransferase
A, B
159Helicobacter pyloriMutation(s): 0 
Gene Names: BXP09_04485CV723_04510
EC: 2.4
UniProt
Find proteins for A0A2L2I2A6 (Helicobacter pylori)
Explore A0A2L2I2A6 
Go to UniProtKB:  A0A2L2I2A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2L2I2A6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.201α = 90
b = 51.544β = 96.092
c = 82.687γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
ARP/wARPdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Refinement description
  • Version 1.2: 2021-05-26
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references