PDBsum entry 2blc

Oxidoreductase

PDB id: 2blc

Contents

Protein chain

215 a.a. *

Ligands

NDP

CP7

MES

Waters ×209

* Residue conservation analysis

PDB id:

2blc

Name:

Oxidoreductase

Title:

Sp21 double mutant p. Vivax dihydrofolate reductase in complex with des-chloropyrimethamine

Structure:

Dihydrofolate reductase-thymidylate synthase. Chain: a. Synonym: dihydrofolate reductase. Engineered: yes

Source:

Plasmodium vivax. Organism_taxid: 5855. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.25Å R-factor: 0.215 R-free: 0.280

Authors:

P.Kongsaeree,P.Khongsuk,U.Leartsakulpanich,P.Chitnumsub, B.Tarnchompoo,M.D.Walkinshaw,Y.Yuthavong

Key ref:

P.Kongsaeree et al. (2005). Crystal structure of dihydrofolate reductase from Plasmodium vivax: pyrimethamine displacement linked with mutation-induced resistance. Proc Natl Acad Sci U S A, 102, 13046-13051. PubMed id: 16135570 DOI: 10.1073/pnas.0501747102

Date:

03-Mar-05 Release date: 07-Sep-05

Protein chain

O02604  (DRTS_PLAVI) -  Bifunctional dihydrofolate reductase-thymidylate synthase from Plasmodium vivax

Seq: 623 a.a.

Struc: 215 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.1.5.1.3 - dihydrofolate reductase.
• Pathway: Folate Coenzymes
• Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH + H⁺

(6S)-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 7,8-dihydrofolate + NADPH + H(+)

• Enzyme class 3: E.C.2.1.1.45 - thymidylate synthase.

Pathway:

• Reaction: dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate = 7,8-dihydrofolate + dTMP

dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate (Bound ligand (Het Group name = CP7) matches with 44.00% similarity) = 7,8-dihydrofolate + dTMP (Bound ligand (Het Group name = NDP) matches with 40.82% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0501747102

Proc Natl Acad Sci U S A 102:13046-13051 (2005)

PubMed id: 16135570

Crystal structure of dihydrofolate reductase from Plasmodium vivax: pyrimethamine displacement linked with mutation-induced resistance.

P.Kongsaeree, P.Khongsuk, U.Leartsakulpanich, P.Chitnumsub, B.Tarnchompoo, M.D.Walkinshaw, Y.Yuthavong.

ABSTRACT

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.

Selected figure(s)

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.

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.

Figures were selected by an automated process.