1E92 | pdb_00001e92

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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/88584
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01782
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth C] Focus chain N [auth D]
HBI Query on HBI Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], M [auth C], O [auth D]	7,8-DIHYDROBIOPTERIN C₉ H₁₃ N₅ O₃ FEMXZDUTFRTWPE-DZSWIPIPSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain O [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain P [auth D] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D]	I [auth B], J [auth B], K [auth B], P [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

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

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-10-05

Deposition Author(s):

Schuettelkopf, A.W.

Hunter, W.N.

Revision History (Full details and data files)

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
Version 1.4: 2023-12-13
Changes: Advisory, Data collection, Database references, Other, Refinement description