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PDBsum entry 2blc
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Oxidoreductase
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PDB id
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2blc
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References listed in PDB file
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Key reference
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Title
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Crystal structure of dihydrofolate reductase from plasmodium vivax: pyrimethamine displacement linked with mutation-Induced resistance.
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Authors
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P.Kongsaeree,
P.Khongsuk,
U.Leartsakulpanich,
P.Chitnumsub,
B.Tarnchompoo,
M.D.Walkinshaw,
Y.Yuthavong.
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Ref.
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Proc Natl Acad Sci U S A, 2005,
102,
13046-13051.
[DOI no: ]
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PubMed id
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Abstract
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Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR)
as well as other malarial parasites, but its use as antimalarial is hampered by
the widespread high resistance. Comparison of the crystal structures of PvDHFR
from wild-type and the Pyr-resistant (SP21, Ser-58 --> Arg + Ser-117 --> Asn)
strain as complexes with NADPH and Pyr or its analog lacking p-Cl (Pyr20)
clearly shows that the steric conflict arising from the side chain of Asn-117 in
the mutant enzyme, accompanied by the loss of binding to Ser-120, is mainly
responsible for the reduction in binding of Pyr. Pyr20 still effectively
inhibits both the wild-type and SP21 proteins, and the x-ray structures of these
complexes show how Pyr20 fits into both active sites without steric strain.
These structural insights suggest a general approach for developing new
generations of antimalarial DHFR inhibitors that, by only occupying substrate
space of the active site, would retain binding affinity with the mutant enzymes.
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Figure 1.
Fig. 1. Crystal structure of the DHFR domain of P. vivax.
(A) Structure of P. vivax DHFR complexed with NADPH and Pyr;
 -helices are in red,
and  -strands are in blue,
including the Insert-1 loop and the Insert-2 -helix. The carbons,
nitrogen, oxygen, and chlorine atoms of Pyr and NADPH are shown
in yellow, blue, red, and magenta, respectively. (B) Comparison
of the DHFR domains from P. vivax (green) and P. falciparum
(magenta). The superimposed structures demonstrate overall
structural similarity with major deviation in the insert regions.
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Figure 2.
Fig. 2. Pyr bound in the PvDHFR active site. The Pyr and
NADPH cofactor are shown as balls and sticks with carbon,
nitrogen, and chlorine colored yellow, blue, and magenta,
respectively. (A) Pyr binding with the WT PvDHFR. Interactions
between the enzyme and the pyrimidine ring of the inhibitor
include electrostatic interactions and H-bonds indicated by
dotted lines. Numbers next to the lines indicate distances in
Å. (B) Pyr binding with the SP21 double-mutant PvDHFR.
Interactions around the pyrimidine ring are similar to the WT
enzyme. The mutation at codon 117 from Ser to Asn increases a
steric factor in the active site, and, as a result, the
positions of both NADPH and Pyr are perturbed from their optimum
binding, reducing the efficiency of Pyr by as much as 300-fold.
(C) Superposition of Pyr-binding sites in the WT PvDHFR (green)
and the SP21 double-mutant enzyme (orange) with a rmsd of 0.53
Å. While the position of pyrimidine is held in the same
place, the mutation at S117N causes the displacement of
p-chlorophenyl moiety of Pyr from its optimal binding with the
p-Cl atom shifted by 1.1 Å and the torsion plane between
the two rings twisted by -32°. The mutation also caused a
local main-chain movement of residues 118 -125 (0.60 -1.88
Å), with respect to the WT enzyme. The mutation at codon
58 from Ser to Arg is not in proximity with the Pyr-binding site.
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