PDBsum entry 3fns

Hydrolase

PDB id: 3fns

Contents

Protein chains

325 a.a. *

Metals

_ZN ×6

Waters ×104

* Residue conservation analysis

PDB id:

3fns

Name:

Hydrolase

Title:

Crystal structure of histo-aspartic protease (hap) from plasmodium falciparum

Structure:

Hap protein. Chain: a, b. Fragment: histo-aspartic protease (hap). Engineered: yes

Source:

Plasmodium falciparum 3d7. Organism_taxid: 36329. Gene: hap, pf14_0078. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.226 R-free: 0.274

Authors:

P.Bhaumik,A.Gustchina,A.Wlodawer

Key ref:

P.Bhaumik et al. (2009). Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum. J Mol Biol, 388, 520-540. PubMed id: 19285084 DOI: 10.1016/j.jmb.2009.03.011

Date:

26-Dec-08 Release date: 12-May-09

Protein chains

Q8IM15  (Q8IM15_PLAF7) -  Plasmepsin III from Plasmodium falciparum (isolate 3D7)

Seq: 451 a.a.

Struc: 325 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.23.39 - plasmepsin Ii.
• Reaction: Hydrolysis of the bonds linking certain hydrophobic residues in hemoglobin or globin. Also cleaves small molecules substrates such as Ala-Leu-Glu-Arg-Thr-Phe-|-Phe(NO(2))-Ser-Phe-Pro-Thr.

DOI no: 10.1016/j.jmb.2009.03.011

J Mol Biol 388:520-540 (2009)

PubMed id: 19285084

Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum.

P.Bhaumik, H.Xiao, C.L.Parr, Y.Kiso, A.Gustchina, R.Y.Yada, A.Wlodawer.

ABSTRACT

The structures of recombinant histo-aspartic protease (HAP) from malaria-causing parasite Plasmodium falciparum as apoenzyme and in complex with two inhibitors, pepstatin A and KNI-10006, were solved at 2.5-, 3.3-, and 3.05-A resolutions, respectively. In the apoenzyme crystals, HAP forms a tight dimer not seen previously in any aspartic protease. The interactions between the monomers affect the conformation of two flexible loops, the functionally important "flap" (residues 70-83) and its structural equivalent in the C-terminal domain (residues 238-245), as well as the orientation of helix 225-235. The flap is found in an open conformation in the apoenzyme. Unexpectedly, the active site of the apoenzyme contains a zinc ion tightly bound to His32 and Asp215 from one monomer and to Glu278A from the other monomer, with the coordination of Zn resembling that seen in metalloproteases. The flap is closed in the structure of the pepstatin A complex, whereas it is open in the complex with KNI-10006. Although the binding mode of pepstatin A is significantly different from that in other pepsin-like aspartic proteases, its location in the active site makes unlikely the previously proposed hypothesis that HAP is a serine protease. The binding mode of KNI-10006 is unusual compared with the binding of other inhibitors from the KNI series to aspartic proteases. The novel features of the HAP active site could facilitate design of specific inhibitors used in the development of antimalarial drugs.

Selected figure(s)

Figure 1.
Fig. 1. Inhibitors of HAP used in this study. (a) Chemical diagrams of pepstatin A and KNI-10006. (b) Initial F[o] − F[c] omit maps for pepstatin A and KNI-10006 contoured at the 1.9σ level, with the final models superimposed.

Figure 10.
Fig. 10. Active site of apo HAP and its complexes with pepstatin A and KNI-10006. The active-site residues are shown in stick representation. (a) A close-up view of the active site of apo HAP. The Zn ion (purple) and the important water molecules (pink) are shown as spheres. (b) A comparison of the active sites of apo HAP and the metalloprotease DppA (d-aminopeptidase). (c) A comparison of the active sites of apo HAP (purple) and its complex with pepstatin A (cyan) based on a superposition of protein C^α atoms. (d) A comparison of the active sites of pepstatin A complexes of HAP (cyan) and pepsin (orange). This superposition is based on protein C^α atoms. (e) Overlay based on a superposition of the identical functional groups in the active sites of HAP (cyan) and pepsin (orange) complexed to pepstatin A. (f) Hydrogen bonding of the statine hydroxyls with the catalytic residues in HAP (cyan) and pepsin (orange). (g) Comparison of the active sites of HAP apoenzyme (pink) and its complexes with pepstatin A (cyan) and KNI-10006 (green). Only the central statine residue of pepstatin A is shown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 388, 520-540) copyright 2009.

Figures were selected by an automated process.