1CJB

MALARIAL PURINE PHOSPHORIBOSYLTRANSFERASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The 2.0 A structure of malarial purine phosphoribosyltransferase in complex with a transition-state analogue inhibitor.

Shi, W., Li, C.M., Tyler, P.C., Furneaux, R.H., Cahill, S.M., Girvin, M.E., Grubmeyer, C., Schramm, V.L., Almo, S.C.

(1999) Biochemistry 38: 9872-9880

  • DOI: 10.1021/bi990664p
  • Primary Citation of Related Structures:  
    1CJB

  • PubMed Abstract: 

    • Malaria is a leading cause of worldwide mortality from infectious disease. Plasmodium falciparum proliferation in human erythrocytes requires purine salvage by hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase). The enzyme is a target for the development of novel antimalarials ...

    Malaria is a leading cause of worldwide mortality from infectious disease. Plasmodium falciparum proliferation in human erythrocytes requires purine salvage by hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase). The enzyme is a target for the development of novel antimalarials. Design and synthesis of transition-state analogue inhibitors permitted cocrystallization with the malarial enzyme and refinement of the complex to 2.0 A resolution. Catalytic site contacts in the malarial enzyme are similar to those of human hypoxanthine-guanine phosphoribosyltransferase (HGPRTase) despite distinct substrate specificity. The crystal structure of malarial HGXPRTase with bound inhibitor, pyrophosphate, and two Mg(2+) ions reveals features unique to the transition-state analogue complex. Substrate-assisted catalysis occurs by ribooxocarbenium stabilization from the O5' lone pair and a pyrophosphate oxygen. A dissociative reaction coordinate path is implicated in which the primary reaction coordinate motion is the ribosyl C1' in motion between relatively immobile purine base and (Mg)(2)-pyrophosphate. Several short hydrogen bonds form in the complex of the enzyme and inhibitor. The proton NMR spectrum of the transition-state analogue complex of malarial HGXPRTase contains two downfield signals at 14.3 and 15.3 ppm. Despite the structural similarity to the human enzyme, the NMR spectra of the complexes reveal differences in hydrogen bonding between the transition-state analogue complexes of the human and malarial HG(X)PRTases. The X-ray crystal structures and NMR spectra reveal chemical and structural features that suggest a strategy for the design of malaria-specific transition-state inhibitors.

    Organizational Affiliation: 

    Albert Einstein College of Medicine, Bronx, New York 10461, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)A, B, C, D231Plasmodium falciparumMutation(s): 0 
EC: 2.4.2.8 (PDB Primary Data), 2.4.2.22 (UniProt)
UniProt
Find proteins for P20035 (Plasmodium falciparum (isolate FCR-3 / Gambia))
Explore P20035 
Go to UniProtKB:  P20035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20035
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IRP
Query on IRP
Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
S [auth D]		(1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE
C11 H15 N4 O7 P
VJTAXXUIRYOXBT-KUBHLMPHSA-N		 Ligand Interaction
POP
Query on POP
Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C],
T [auth D]		PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IRP Binding MOAD:  1CJB Kd: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.49α = 90
b = 110.39β = 90
c = 173.7γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-12-11
    Changes: Derived calculations