5uv1
From Proteopedia
Crystal Structure of (+)-Limonene Synthase Complexed with 2-Fluorogeranyl Diphosphate
Structural highlights
FunctionRLC1_CITSI Catalyzes the conversion of geranyl diphosphate to (+)-(4R)-limonene (PubMed:28272875, PubMed:28272876). Produces exclusively the (+)-enantiomer (PubMed:28272875). Can use neryl diphosphate as substrate (PubMed:28272876). Has no activity with farnesyl diphosphate (PubMed:28272875).[1] [2] Publication Abstract from PubMedThe stereochemical course of monoterpene synthase reactions is thought to be determined early in the reaction sequence by selective binding of distinct conformations of the geranyl diphosphate (GPP) substrate. We explore here formation of early Michaelis complexes of the (+)-limonene synthase [(+)-LS] from Citrus sinensis using monofluorinated substrate analogues 2-fluoro-GPP (FGPP) and 2-fluoroneryl diphosphate (FNPP). Both are competitive inhibitors for (+)-LS with KI values of 2.4 +/- 0.5 and 39.5 +/- 5.2 muM, respectively. The KI values are similar to the KM for the respective nonfluorinated substrates, indicating that fluorine does not significantly perturb binding of the ligand to the enzyme. FGPP and FNPP are also substrates, but with dramatically reduced rates (kcat values of 0.00054 +/- 0.00005 and 0.00024 +/- 0.00002 s-1, respectively). These data are consistent with a stepwise mechanism for (+)-LS involving ionization of the allylic GPP substrate to generate a resonance-stabilized carbenium ion in the rate-limiting step. Crystals of apo-(+)-LS were soaked with FGPP and FNPP to obtain X-ray structures at 2.4 and 2.2 A resolution, respectively. The fluorinated analogues are found anchored in the active site through extensive interactions involving the diphosphate, three metal ions, and three active-site Asp residues. Electron density for the carbon chains extends deep into a hydrophobic pocket, while the enzyme remains mostly in the open conformation observed for the apoprotein. While FNPP was found in multiple conformations, FGPP, importantly, was in a single, relatively well-defined, left-handed screw conformation, consistent with predictions for the mechanism of stereoselectivity in the monoterpene synthases. Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed by (+)-Limonene Synthase from Citrus sinensis Using Fluorinated Substrate Analogues.,Kumar RP, Morehouse BR, Matos JO, Malik K, Lin H, Krauss IJ, Oprian DD Biochemistry. 2017 Mar 15. doi: 10.1021/acs.biochem.7b00144. PMID:28272876[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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