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Dataset for: High resolution studies of hydride transfer in the ferredoxin:NADP+ reductase superfamily
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posted on 2017-08-30, 04:47 authored by Kelsey M. Kean, Russell A. Carpenter, Vittorio Pandini, Guiliana Zanetti, Andrea R. Hall, Rick Faber, Alessandro Aliverti, Andrew KarplusFerredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme best known for catalyzing the transfer of electrons from ferredoxin (Fd) to NADP+ to make NADPH during photosynthesis. It is also the prototype for a broad enzyme superfamily, including the NADPH oxidases (NOXs) that all catalyze similar FAD-enabled electron transfers between NAD(P)H and one-electron carriers. Here we define further mechanistic details of the NAD(P)H ⇌ FAD hydride-transfer step of the reaction based on spectroscopic studies and high resolution (~1.5 Å) crystallographic views of the nicotinamide-flavin interaction in crystals of corn root FNR Tyr316Ser and Tyr316Ala variants soaked with either nicotinamide, NADP+, or NADPH. The spectra obtained from FNR crystal complexes match those seen in solution and the complexes reveal active site packing interactions and patterns of covalent distortion of the FAD that imply significant active site compression that would favor catalysis. Furthermore, anisotropic B-factors show that the mobility of the C4 atom of the nicotinamide in the FNR:NADP+ complex has a directionality matching that expected for boat-like excursions of the nicotinamide ring thought to enhance hydride transfer. Arguments are made for the relevance of this binding mode to catalysis, and specific consideration is given to how the results extrapolate to provide insight to structure-function relations for the membrane-bound NOX enzymes for which little structural information has been available.
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Categories
- Regenerative medicine (incl. stem cells)
- Biochemistry and cell biology not elsewhere classified
- Plant cell and molecular biology
- Animal cell and molecular biology
- Evolution of developmental systems
- Structural biology (incl. macromolecular modelling)
- Synthetic biology
- Proteomics and intermolecular interactions (excl. medical proteomics)
- Evolutionary biology not elsewhere classified
- Signal transduction
- Cancer cell biology
- Systems biology
- Bioinformatics and computational biology not elsewhere classified
- Computational methods in fluid flow, heat and mass transfer (incl. computational fluid dynamics)
Keywords
Flavoenzymehydride transferenzyme mechanismprotein crystallographyNADPH oxidaseStem CellsBiochemistryMolecular BiologyDevelopmental BiologyStructural BiologySynthetic BiologyProteomics and Intermolecular Interactions (excl. Medical Proteomics)Evolutionary BiologySignal TransductionCancer Cell BiologySystems BiologyBioinformaticsHeat and Mass Transfer Operations
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