PDBsum entry 1qnh

Isomerase/immunosuppressant

PDB id: 1qnh

Contents

Protein chains

169 a.a. *

11 a.a. *

Waters ×213

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The three-Dimensional structure of a plasmodium falciparum cyclophilin in complex with the potent anti-Malarial cyclosporin a.

Authors

M.R.Peterson, D.R.Hall, M.Berriman, J.A.Nunes, G.A.Leonard, A.H.Fairlamb, W.N.Hunter.

Ref.

J Mol Biol, 2000, 298, 123-133. [DOI no: 10.1006/jmbi.2000.3633]

PubMed id

10756109

Abstract

Cyclosporin A (CsA) is a potent anti-malarial compound in vitro and in vivo in mice though better known for its immunosuppressive properties in humans. Crystal structures of wild-type and a double mutant Plasmodium falciparum cyclophilin (PfCyP19 and mPfCyP19) complexed with CsA have been determined using diffraction terms to a resolution of 2.1 A (1 A=0.1 nm). The wild-type has a single PfCyP19/CsA complex per asymmetric unit in space group P1 and refined to an R-work of 0.15 and R-free of 0.19. An altered cyclophilin, with two accidental mutations, Phe120 to Leu in the CsA binding pocket and Leu171 to Trp at the C terminus, presents two complexes per asymmetric unit in the orthorhombic space group P2(1)2(1)2. This refined to an R-work of 0.18 and R-free 0.21. The mutations were identified from the crystallographic analysis and the C-terminal alteration helps to explain the different crystal forms obtained. PfCyP19 shares approximately 61 % sequence identity with human cyclophilin A (hCyPA) and the structures are similar, consisting of an eight-stranded antiparallel beta-barrel core capped by two alpha-helices. The fold creates a hydrophobic active-site, the floor of which is formed by side-chains of residues from four antiparallel beta-strands and the walls from loops and turns. We identified C-H.O hydrogen bonds between the drug and protein that may be an important feature of cyclophilins and suggest a general mode of interaction between hydrophobic molecules. Comparisons with cyclophilin-dipeptide complexes suggests that a specific C-H.O hydrogen bonding interaction may contribute to ligand binding. Residues Ser106, His99 and Asp130, located close to the active site and conserved in most cyclophilins, are arranged in a manner reminiscent of a serine protease catalytic triad. A Ser106Ala mutant was engineered to test the hypothesis that this triad contributes to CyP function. Mutant and wild-type enzymes were found to have similar catalytic properties.

Figure 2.
Figure 2. The PfCyP19/CsA complex. Protein is represented in ribbon form with secondary structure elements helices (red); C-terminal direction, for b-strands (yellow arrows), a section of 3[10] helix (cyan ribbon). The loop segments are numbered 1 to 5. CsA is illustrated as a stick model where carbon positions (black), nitrogen (blue), and oxygen (red). Figure 2, Figure 3, Figure 4, Figure 5 and Figure 6 inclusive were constructed using MOLSCRIPT [Kraulis 1991] and RASTER3D [Merritt and Bacon 1997].

Figure 6.
Figure 6. The difference in the active site between the native (stick model) and the mutant (ball and stick model) highlighting the Phe120Leu mutation in relation to MeVal11 of CsA.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 123-133) copyright 2000.

Secondary reference #1

Title

Detailed characterization of a cyclophilin from the human malaria parasite plasmodium falciparum.

Authors

M.Berriman, A.H.Fairlamb.

Ref.

Biochem J, 1998, 334, 437-445.

PubMed id

9716503