4FYM

Crystal structure of Plasmodium falciparum orotate phosphoribosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Plasmodium falciparum orotate phosphoribosyltransferase with autologous inhibitory protein-protein interactions.

Kumar, S.Krishnamoorthy, K.Mudeppa, D.G.Rathod, P.K.

(2015) Acta Crystallogr F Struct Biol Commun 71: 600-608

  • DOI: https://doi.org/10.1107/S2053230X1500549X
  • Primary Citation of Related Structures:  
    4FYM

  • PubMed Abstract: 

    The most severe form of malaria is caused by the obligate parasite Plasmodium falciparum. Orotate phosphoribosyltransferase (OPRTase) is the fifth enzyme in the de novo pyrimidine-synthesis pathway in the parasite, which lacks salvage pathways. Among all of the malaria de novo pyrimidine-biosynthesis enzymes, the structure of P. falciparum OPRTase (PfOPRTase) was the only one unavailable until now. PfOPRTase that could be crystallized was obtained after some low-complexity sequences were removed. Four catalytic dimers were seen in the asymmetic unit (a total of eight polypeptides). In addition to revealing unique amino acids in the PfOPRTase active sites, asymmetric dimers in the larger structure pointed to novel parasite-specific protein-protein interactions that occlude the catalytic active sites. The latter could potentially modulate PfOPRTase activity in parasites and possibly provide new insights for blocking PfOPRTase functions.


  • Organizational Affiliation

    Department of Chemistry, University of Washington, Seattle, WA 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orotate phosphoribosyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H
266Plasmodium falciparumMutation(s): 0 
Gene Names: oprt
EC: 2.4.2.10
UniProt
Find proteins for Q8N0R1 (Plasmodium falciparum)
Explore Q8N0R1 
Go to UniProtKB:  Q8N0R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N0R1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth D],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
I [auth A],
IA [auth F],
J [auth A],
JA [auth G],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
M [auth B],
MA [auth H],
N [auth B],
NA [auth H],
O [auth B],
OA [auth H],
P [auth B],
Q [auth B],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.769α = 90
b = 152.487β = 90
c = 167.755γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2015-06-03
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description