1E92

Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin

• PDB DOI:  https://doi.org/10.2210/pdb1E92/pdb

• Classification: PTERIDINE REDUCTASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-10-04 Released: 2001-10-05 
• Deposition Author(s): Schuettelkopf, A.W., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

Pteridine Reductase Mechanism Correlates Pterin Metabolism with Drug Resistance in Trypanosomatid Parasites

Gourley, D.G., Schuettelkopf, A.W., Leonard, G.A., Luba, J., Hardy, L.W., Beverley, S.M., Hunter, W.N.

(2001) Nat Struct Biol 8: 521

• PubMed: 11373620 
• DOI: https://doi.org/10.1038/88584
• Primary Citation of Related Structures:  
  1E7W, 1E92


• PubMed Abstract: 
  

Pteridine reductase (PTR1) is a short-chain reductase (SDR) responsible for the salvage of pterins in parasitic trypanosomatids. PTR1 catalyzes the NADPH-dependent two-step reduction of oxidized pterins to the active tetrahydro-forms and reduces susceptibility to antifolates by alleviating dihydrofolate reductase (DHFR) inhibition. Crystal structures of PTR1 complexed with cofactor and 7,8-dihydrobiopterin (DHB) or methotrexate (MTX) delineate the enzyme mechanism, broad spectrum of activity and inhibition by substrate or an antifolate. PTR1 applies two distinct reductive mechanisms to substrates bound in one orientation. The first reduction uses the generic SDR mechanism, whereas the second shares similarities with the mechanism proposed for DHFR. Both DHB and MTX form extensive hydrogen bonding networks with NADP(H) but differ in the orientation of the pteridine.

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Organizational Affiliation: 

The Wellcome Trust Biocentre, University of Dundee, Dundee, DD1 5EH, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 125.94 kDa 
• Atom Count: 8,522 
• Modelled Residue Count: 1,047 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTERIDINE REDUCTASE 1	A, B, C, D	288	Leishmania major	Mutation(s): 0  Gene Names: PTR1, HMTXR, L1063.01, LmjF23.0270, LmjF_23_0270 EC: 1.1.1.253 (PDB Primary Data), 1.5.1.33 (UniProt)
UniProt
Find proteins for Q01782 (Leishmania major) Explore Q01782  Go to UniProtKB:  Q01782

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], G [auth B], L [auth C], N [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
HBI	F [auth A], H [auth B], M [auth C], O [auth D]	7,8-DIHYDROBIOPTERIN C9 H13 N5 O3 FEMXZDUTFRTWPE-DZSWIPIPSA-N
EDO	I [auth B], J [auth B], K [auth B], P [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.338	α = 90
b = 103.801	β = 90
c = 137.412	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-05 
Deposition Author(s): Schuettelkopf, A.W., Hunter, W.N.

Revision History  

• Version 1.0: 2001-10-05
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Advisory, Data collection, Experimental preparation, Other