PDBsum entry 2bfp

Oxidoreductase

PDB id: 2bfp

Contents

Protein chains

267 a.a. *

Ligands

NAP ×4

H4B ×4

EDO ×6

Waters ×152

* Residue conservation analysis

PDB id:

2bfp

Name:

Oxidoreductase

Title:

Leishmania major pteridine reductase 1 in complex with NADP and tetrahydrobiopterin

Structure:

Pteridine reductase 1. Chain: a, b, c, d. Synonym: h region methotrexate resistance protein. Engineered: yes

Source:

Leishmania major. Organism_taxid: 5664. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.55Å R-factor: 0.200 R-free: 0.238

Authors:

A.W.Schuettelkopf,W.N.Hunter

Key ref:

A.W.Schüttelkopf et al. (2005). Structures of Leishmania major pteridine reductase complexes reveal the active site features important for ligand binding and to guide inhibitor design. J Mol Biol, 352, 105-116. PubMed id: 16055151 DOI: 10.1016/j.jmb.2005.06.076

Date:

10-Dec-04 Release date: 31-Aug-05

Protein chains

Q01782  (PTR1_LEIMA) -  Pteridine reductase 1 from Leishmania major

Seq: 288 a.a.

Struc: 267 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.5.1.33 - pteridine reductase.
• Reaction: (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin + 2 NADP⁺ = L-erythro- biopterin + 2 NADPH + 2 H⁺

(6R)-L-erythro-5,6,7,8-tetrahydrobiopterin + 2 × NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = L-erythro- biopterin + 2 × NADPH + 2 × H(+)

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

Added reference

DOI no: 10.1016/j.jmb.2005.06.076

J Mol Biol 352:105-116 (2005)

PubMed id: 16055151

Structures of Leishmania major pteridine reductase complexes reveal the active site features important for ligand binding and to guide inhibitor design.

A.W.Schüttelkopf, L.W.Hardy, S.M.Beverley, W.N.Hunter.

ABSTRACT

Pteridine reductase (PTR1) is an NADPH-dependent short-chain reductase found in parasitic trypanosomatid protozoans. The enzyme participates in the salvage of pterins and represents a target for the development of improved therapies for infections caused by these parasites. A series of crystallographic analyses of Leishmania major PTR1 are reported. Structures of the enzyme in a binary complex with the cofactor NADPH, and ternary complexes with cofactor and biopterin, 5,6-dihydrobiopterin, and 5,6,7,8-tetrahydrobiopterin reveal that PTR1 does not undergo any major conformational changes to accomplish binding and processing of substrates, and confirm that these molecules bind in a single orientation at the catalytic center suitable for two distinct reductions. Ternary complexes with cofactor and CB3717 and trimethoprim (TOP), potent inhibitors of thymidylate synthase and dihydrofolate reductase, respectively, have been characterized. The structure with CB3717 reveals that the quinazoline moiety binds in similar fashion to the pterin substrates/products and dominates interactions with the enzyme. In the complex with TOP, steric restrictions enforced on the trimethoxyphenyl substituent prevent the 2,4-diaminopyrimidine moiety from adopting the pterin mode of binding observed in dihydrofolate reductase, and explain the inhibition properties of a range of pyrimidine derivates. The molecular detail provided by these complex structures identifies the important interactions necessary to assist the structure-based development of novel enzyme inhibitors of potential therapeutic value.

Selected figure(s)

Figure 2.
Figure 2. The chemical structures of three PTR1 inhibitors: methotrexate, CB3717 and trimethoprim. The molecules are depicted in a similar orientation in all Figures. The methotrexate molecule is depicted with the pterin-ring flipped about the N2-N5 axis relative to other pterins as actually observed in the PTR1 active site.

Figure 6.
Figure 6. CB3717 binding to LmPTR1. (a) Stereoview showing the omit difference density map (contoured at 2.4s) as described for Figure 3. The same color scheme as Figure 3 is used with the addition that the glutamate tail of the inhibitor is red and broken lines represent potential hydrogen bonds. Phe113 is depicted as a semitransparent object. (b) A representation of the active site with the ligand in similar fashion to Figure 4.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 105-116) copyright 2005.

Figures were selected by the author.