The crystal structures of Phascolopsis gouldii wild type and L98Y methemerythrins: structural and functional alterations of the O₂ binding pocket

Abstract

Reported are the X-ray crystal structures of recombinant Phascolopsis gouldii methemerythrin (1.8-Å resolution) and the structure of an O₂-binding-pocket mutant, L98Y methemerythrin (2.1-Å resolution). The L98Y hemerythrin (Hr) has a greatly enhanced O₂ affinity, a slower O₂ dissociation rate, a larger solvent deuterium isotope effect on this rate, and a greater resistance to autoxidation relative to the wild-type protein. The crystal structures show that the hydrophobic binding pocket of Hr can accommodate substitution of a leucyl by a tyrosyl side chain with relatively minor structural rearrangements. UV/vis and resonance Raman spectra show that in solution L98Y methemerythrin contains a mixture of two diiron site structures differing by the absence or presence of an Fe(III)-coordinated phenolate. However, in the crystal, only one L98Y diiron site structure is seen, in which the Y98 hydroxyl is not a ligand, but instead forms a hydrogen bond to a terminal hydroxo/aqua ligand to the nearest iron. Based on this crystal structure, we propose that in the oxy form of L98Y hemerythrin the non-polar nature of the binding pocket favors localization of the Y98 hydroxyl near the O₂ binding site, where it can donate a hydrogen bond to the hydroperoxo ligand. The stabilizing Y98OH-O₂H^– interaction would account for all of the altered O₂ binding properties of L98Y Hr listed above.