5KAM

Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with Inosine 5' monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures and inhibition of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltransferase.

Teran, D.Hockova, D.Cesnek, M.Zikova, A.Naesens, L.Keough, D.T.Guddat, L.W.

(2016) Sci Rep 6: 35894-35894

  • DOI: https://doi.org/10.1038/srep35894
  • Primary Citation of Related Structures:  
    5JSQ, 5JV5, 5K51, 5KAM, 5KAP

  • PubMed Abstract: 

    Human African Trypanosomiasis (HAT) is a life-threatening infectious disease caused by the protozoan parasite, Trypanosoma brucei (Tbr). Due to the debilitating side effects of the current therapeutics and the emergence of resistance to these drugs, new medications for this disease need to be developed. One potential new drug target is 6-oxopurine phosphoribosyltransferase (PRT), an enzyme central to the purine salvage pathway and whose activity is critical for the production of the nucleotides (GMP and IMP) required for DNA/RNA synthesis within this protozoan parasite. Here, the first crystal structures of this enzyme have been determined, these in complex with GMP and IMP and with three acyclic nucleoside phosphonate (ANP) inhibitors. The K i values for GMP and IMP are 30.5 μM and 77 μM, respectively. Two of the ANPs have K i values considerably lower than for the nucleotides, 2.3 μM (with guanine as base) and 15.8 μM (with hypoxanthine as base). The crystal structures show that when two of the ANPs bind, they induce an unusual conformation change to the loop where the reaction product, pyrophosphate, is expected to bind. This and other structural differences between the Tbr and human enzymes suggest selective inhibitors for the Tbr enzyme can be designed.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine phosphoribosyltransferaseA,
B [auth C]
216Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: HGPRT
EC: 2.4.2.8
UniProt
Find proteins for Q07010 (Trypanosoma brucei brucei)
Explore Q07010 
Go to UniProtKB:  Q07010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07010
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download Ideal Coordinates CCD File 
C [auth A],
H [auth C]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth C],
J [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth C],
L [auth C],
M [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 
  • Space Group: P 2 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.054α = 90
b = 109.819β = 90
c = 45.292γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASESphasing
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description