title: Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.
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.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
authors.forename: Arthur H
authors.initials: AH
authors.lastname: Robbins
authors.forename: Ben M
authors.initials: BM
authors.lastname: Dunn
authors.forename: Mavis
authors.initials: M
authors.lastname: Agbandje-McKenna
authors.forename: Robert
authors.initials: R
authors.lastname: McKenna
mesh_terms: 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
chemical_list: D015800:Protozoan Proteins; D014867:Water; D001224:Aspartic Acid; D016282:Aspartic Acid Endopeptidases; C100637:plasmepsin II