Spectroscopic and Computational Evaluation of the Structure
of the High-Spin Fe(IV)-Oxo Intermediates in Taurine:
r-Ketoglutarate Dioxygenase from Escherichia coli and Its
His99Ala Ligand Variant
Sebastian Sinnecker,
²
Nina Svensen,
‡
Eric W. Barr,
‡
Shengfa Ye,
²,§
J. Martin Bollinger, Jr.,*
,‡,|
Frank Neese,*
,²,§
and Carsten Krebs*
,‡,|
Contribution from the Max-Planck Institut fu ¨r Bioanorganische Chemie, D-45470 Mu ¨lheim an
der Ruhr, Germany, Department of Biochemistry and Molecular Biology, The PennsylVania State
UniVersity, UniVersity Park, PennsylVania 16802, Institut fu ¨r Physikalische und Theoretische
Chemie, UniVersita ¨t Bonn, D-53115 Bonn, Germany, and Department of Chemistry,
The PennsylVania State UniVersity, UniVersity Park, PennsylVania 16802
Received November 9, 2006; E-mail: jmb21@psu.edu; neese@thch.uni-bonn.de; ckrebs@psu.edu
Abstract: The Fe(II)- and R-ketoglutarate (RKG)-dependent dioxygenases activate O2 for cleavage of
unactivated C-H bonds in their substrates. The key intermediate that abstracts hydrogen in the reaction
of taurine:RKG dioxygenase (TauD), a member of this enzyme family, was recently characterized. The
intermediate, denoted J, was shown to contain an iron(IV)-oxo unit. Other important structural features of
J, such as the number, identity, and disposition of ligands in the Fe(IV) coordination sphere, are not yet
understood. To probe these important structural features, a series of models for J with the Fe(IV) ion
coordinated by the expected two imidazole (from His99 and His255), two carboxylate (succinate and
Asp101), and oxo ligands have been generated by density functional theory (DFT) calculations, and
spectroscopic parameters (Mo ¨ ssbauer isomer shift, quadrupole splitting, and asymmetry parameter,
57
Fe
hyperfine coupling tensor, and zero field splitting parameters, D and E/D) have been calculated for each
model. The calculated parameters of distorted octahedral models for J, in which one of the carboxylates
serves as a monodentate ligand and the other as a bidentate ligand, and a trigonal bipyramidal model, in
which both carboxylates serve as monodentate ligands, agree well with the experimental parameters,
whereas the calculated parameters of a square pyramidal model, in which the oxo ligand is in the equatorial
plane, are inconsistent with the data. Similar analysis of the Fe(IV) complex generated in the variant protein
with His99, the residue that contributes the imidazole ligand cis to the oxo group, replaced by alanine
suggests that the deleted imidazole is replaced by a water ligand. This work lends credence to the idea
that the combination of Mo ¨ ssbauer spectroscopy and DFT calculations can provide detailed structural
information for reactive intermediates in the catalytic cycles of iron enzymes.
Introduction
The Fe(II)- and R-ketoglutarate-dependent oxygenases are a
large family of enzymes
1-4
that catalyze steps in, among other
processes, the biosyntheses of antibiotics
5
and collagen,
6,7
the
repair of alkylated DNA,
8,9
the detection of and response to
oxygen insufficiency (hypoxia),
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and the regulation of gene
expression.
18-20
They couple the reductive activation of dioxy-
²
Max-Planck Institut fu ¨r Bioanorganische Chemie.
‡
Department of Biochemistry and Molecular Biology, The Pennsylvania
State University.
§
Universita ¨t Bonn.
|
Department of Chemistry, The Pennsylvania State University.
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Published on Web 04/24/2007
6168 9 J. AM. CHEM. SOC. 2007, 129, 6168-6179 10.1021/ja067899q CCC: $37.00 © 2007 American Chemical Society