3PH7

Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate

Replaces:  3MYS

Summary for 3PH7

• Entry DOI: 10.2210/pdb3ph7/pdb
• Related: 3LDW
• Descriptor: Farnesyl pyrophosphate synthase, GERANYLGERANYL DIPHOSPHATE (3 entities in total)
• Functional Keywords: malaria, farnesyl pyrophosphate synthase diphosphate, lyase, structural genomics, structural genomics consortium, sgc
• Biological source: Plasmodium vivax
• Total number of polymer chains: 4
• Total formula weight: 186664.77

Authors

Wernimont, A.K.,Dunford, J.,Lew, J.,Zhao, Y.,Kozieradzki, I.,Cossar, D.,Schapiro, M.,Bochkarev, A.,Arrowsmith, C.H.,Bountra, C.,Weigelt, J.,Edwards, A.M.,Hui, R.,Artz, J.D.,Structural Genomics Consortium (SGC) (deposition date: 2010-11-03, release date: 2010-11-17, Last modification date: 2024-02-21)

Primary citation

Artz, J.D.,Wernimont, A.K.,Dunford, J.E.,Schapira, M.,Dong, A.,Zhao, Y.,Lew, J.,Russell, R.G.,Ebetino, F.H.,Oppermann, U.,Hui, R.
Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites.
J.Biol.Chem., 286:3315-3322, 2011

PubMed Abstract: We present here a study of a eukaryotic trans-prenylsynthase from the malaria pathogen Plasmodium vivax. Based on the results of biochemical assays and contrary to previous indications, this enzyme catalyzes the production of geranylgeranyl pyrophosphate (GGPP) rather than farnesyl pyrophosphate (FPP). Structural analysis shows that the product length is constrained by a hydrophobic cavity formed primarily by a set of residues from the same subunit as the product as well as at least one other from the dimeric partner. Furthermore, Plasmodium GGPP synthase (GGPPS) can bind nitrogen-containing bisphosphonates (N-BPs) strongly with the energetically favorable cooperation of three Mg(2+), resulting in inhibition by this class of compounds at IC(50) concentrations below 100 nM. In contrast, human and yeast GGPPSs do not accommodate a third magnesium atom in the same manner, resulting in their insusceptibility to N-BPs. This differentiation is in part attributable to a deviation in a conserved motif known as the second aspartate-rich motif: whereas the aspartates at the start and end of the five-residue motif in FFPP synthases and P. vivax GGPPSs both participate in the coordination of the third Mg(2+), an asparagine is featured as the last residue in human and yeast GGPPSs, resulting in a different manner of interaction with nitrogen-containing ligands.

PubMed: 21084289
DOI: 10.1074/jbc.M109.027235

Experimental method

X-RAY DIFFRACTION (2.5 Å)