Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.
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.
Robbins
Arthur H
AH
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
Dunn
Ben M
BM
Agbandje-McKenna
Mavis
M
McKenna
Robert
R
D000818:Animals; D001224:Aspartic Acid / Q000737:chemistry*; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry*; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004583:Electrons; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010963:Plasmodium falciparum / Q000201:enzymology*; D011487:Protein Conformation; D015800:Protozoan Proteins / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D015800:Protozoan Proteins; D014867:Water; D001224:Aspartic Acid; D016282:Aspartic Acid Endopeptidases; C100637:plasmepsin II