6EDH

Taurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinate

Summary for 6EDH

• Entry DOI: 10.2210/pdb6edh/pdb
• Descriptor: Alpha-ketoglutarate-dependent taurine dioxygenase, ACETATE ION, oxovanadium(2+), ... (9 entities in total)
• Functional Keywords: hydroxylase, 2-oxo-glutarate, vanadyl ion, oxidoreductase
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 2
• Total formula weight: 65881.72

Authors

Davis, K.M.,Altmyer, M.,Boal, A.K. (deposition date: 2018-08-09, release date: 2019-08-21, Last modification date: 2024-04-03)

Primary citation

Davis, K.M.,Altmyer, M.,Martinie, R.J.,Schaperdoth, I.,Krebs, C.,Bollinger Jr., J.M.,Boal, A.K.
Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD.
Biochemistry, 58:4218-4223, 2019

PubMed Abstract: Iron(II)- and 2-(oxo)-glutarate-dependent (Fe/2OG) oxygenases catalyze a diverse array of oxidation reactions via a common iron(IV)-oxo (ferryl) intermediate. Although the intermediate has been characterized spectroscopically, its short lifetime has precluded crystallograhic characterization. In solution, the ferryl was first observed directly in the archetypal Fe/2OG hydroxylase, taurine:2OG dioxygenase (TauD). Here, we substitute the iron cofactor of TauD with the stable vanadium(IV)-oxo (vanadyl) ion to obtain crystal structures mimicking the key ferryl complex. Intriguingly, whereas the structure of the TauD·(V-oxo)·succinate·taurine complex exhibits the expected orientation of the V≡O bond- to the His255 ligand and toward the C-H bond to be cleaved, in what has been termed the in-line configuration-the TauD·(V-oxo) binary complex is best modeled with its oxo ligand to Asp101. This off-line-like configuration is similar to one recently posited as a means to avoid hydroxylation in Fe/2OG enzymes that direct other outcomes, though neither has been visualized in an Fe/2OG structure to date. Whereas an off-line ( to the proximal His) or off-line-like ( to the carboxylate ligand) ferryl is unlikely to be important in the hydroxylation reaction of TauD, the observation that the ferryl may deviate from an in-line orientation in the absence of the primary substrate may explain the enzyme's mysterious self-hydroxylation behavior, should the oxo ligand lie to His99. This finding reinforces the potential for analogous functional off-line oxo configurations in halogenases, desaturases, and/or cyclases.

PubMed: 31503454
DOI: 10.1021/acs.biochem.9b00598

Experimental method

X-RAY DIFFRACTION (1.73000401657 Å)