6EDH image
Deposition Date 2018-08-09
Release Date 2019-08-21
Last Version Date 2024-04-03
Entry Detail
PDB ID:
6EDH
Keywords:
Title:
Taurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinate
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.73 Å
R-Value Free:
0.20
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Alpha-ketoglutarate-dependent taurine dioxygenase
Gene (Uniprot):tauD
Chain IDs:A, B
Chain Length:283
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
Primary Citation
Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD.
Biochemistry 58 4218 4223 (2019)
PMID: 31503454 DOI: 10.1021/acs.biochem.9b00598

Abstact

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·(VIV-oxo)·succinate·taurine complex exhibits the expected orientation of the V≡O bond-trans to the His255 ligand and toward the C-H bond to be cleaved, in what has been termed the in-line configuration-the TauD·(VIV-oxo) binary complex is best modeled with its oxo ligand trans 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 (trans to the proximal His) or off-line-like (trans 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 trans to His99. This finding reinforces the potential for analogous functional off-line oxo configurations in halogenases, desaturases, and/or cyclases.

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