PDBsum entry 1vj3

Oxidoreductase

PDB id: 1vj3

Contents

Protein chain

205 a.a. *

Ligands

NDP

TAB

Waters ×75

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the pneumocystis carinii dihydrofolate reductase cofactor complex with tab, A highly selective antifolate.

Authors

V.Cody, D.Chan, N.Galitsky, D.Rak, J.R.Luft, W.Pangborn, S.F.Queener, C.A.Laughton, M.F.Stevens.

Ref.

Biochemistry, 2000, 39, 3556-3564. [DOI no: 10.1021/bi9924563]

PubMed id

10736154

Abstract

The crystal structure of the ternary complex of NADPH, the potent antifolate [2, 4-diamino-5-¿3-[3-(2-acetyloxyethyl)-3-benzyltriazen-1-yl]-4 -chloroph enyl¿-6-ethylpyrimidine] (TAB, 1) and Pneumocystis carinii dihydrofolate reductase (pcDHFR), refined to 2.1 A resolution, reveals that TAB binds similar to the antifolates trimethoprim and methotrexate. These data also reveal multiple conformations for the binding geometry of TAB with two preferred orientations of the acetyloxy and benzyl groups that results from a 180 degrees rotation about the N2-N3 triazenyl bond. The methyl of the acetyloxy and benzyl ring of TAB probes large hydrophobic regions of the p-aminobenzoyl folate binding pocket of the active site, in particular the region near Phe69, which is unique to the pcDHFR sequence. These results confirm prior molecular modeling investigations of the binding of TAB to pcDHFR that identified four low-energy binding geometries, two involving rotations about the terminal N(2)-N(3) triazenyl linkage and two involving atropisomerism about the pivotal pyrimethamine-phenyl bond. The primary differences in the molecular dynamics (MD) models and those observed in this crystal complex result from small conformational changes in active-site residues on energy minimization. However, two MD models place the acetyloxy and benzyl ring groups in a region of the active site between the cofactor-binding region and the p-aminobenzoyl folate pocket; an orientation never observed in any DHFR crystal structure to date. These conformers interact with solvent near the enzyme surface and are probably not observed due to the loss of specific hydrogen bonds with the enzyme. The high species pcDHFR selectivity of TAB could be the result of ligand flexibility that enables multiple binding orientations at the enzyme active site. Further modification of the acetyloxy region of TAB could increase its potency and selectivity for pcDHFR.

Secondary reference #1

Title

Ligand-Induced conformational changes in the crystal structures of pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+.

Authors

V.Cody, N.Galitsky, D.Rak, J.R.Luft, W.Pangborn, S.F.Queener.

Ref.

Biochemistry, 1999, 38, 4303-4312. [DOI no: 10.1021/bi982728m]

PubMed id

10194348

Secondary reference #2

Title

The structure of pneumocystis carinii dihydrofolate reductase to 1.9 a resolution.

Authors

J.N.Champness, A.Achari, S.P.Ballantine, P.K.Bryant, C.J.Delves, D.K.Stammers.

Ref.

Structure, 1994, 2, 915-924. [DOI no: 10.1016/S0969-2126(94)00093-X]

PubMed id

7866743

Figure 5.
Figure 5. Chemical structures of the inhibitors (a) trimethoprim and (b) piritrexim.

Figure 6.
Figure 6. Binding of inhibitor molecules within the active site of P. carinii DHFR. (a) Electron density difference map from difference Fourier analysis of the enzyme-trimethoprim complex contoured at the 2.5s density level with the trimethoprim skeletal model superimposed. (b) The corresponding difference map for the enzyme-piritrexim complex difference Fourier, contoured at a similar density level. (c)Comparison of the binding of the inhibitors trimethoprim (yellow) and piritrexim (blue) to P. carinii DHFR by superimposing the two complexes. Regions where the overlap between the two structures is closest are shown as white.

The above figures are reproduced from the cited reference with permission from Cell Press