Download MendeleyCrystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.
Robbins, A.H., Dunn, B.M., Agbandje-McKenna, M., McKenna, R.(2009) Acta Crystallogr D Biol Crystallogr 65: 294-296
- PubMed: 19237752
- DOI: https://doi.org/10.1107/S0907444908041632
- Primary Citation of Related Structures:
3F9Q - PubMed Abstract:
The carboxylate atoms of the two catalytic aspartic acid residues in aspartic proteases are nearly coplanar and in the uncomplexed form share an in-plane nucleophilic water molecule that is central to the mechanism of these enzymes. This note reports that while reviewing the electron-density maps derived from the deposited data for uncomplexed plasmepsin II from Plasmodium falciparum [Asojo et al. (2003), J. Mol. Biol. 327, 173-181; PDB code 1lf4], it was discovered that the aspartic acid residues in this structure should in fact be distinctly noncoplanar. The crystallographic model from the deposited coordinates has been re-refined against the 1.9 A resolution published diffraction data to an R(cryst) of 21.2% and an R(free) of 22.2%. The catalytic water molecule is present, but the plane of the carboxylate group of Asp214 is rotated by 66 degrees from its original position.
Organizational Affiliation:
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
