Examination of the Nickel Site Structure and Reaction Mechanism in <i>Streptomyces</i> <i>seoulensis </i>Superoxide Dismutase

Choudhury, Suranjan Bhanja; Lee, Jin-Won; Davidson, Gerard; Yim, Yang In; Bose, Kurethara S.; Sharma, Manju; Kang, Shinjae; Cabelli, Diane E.; Maroney, Michael J.

doi:10.1021/bi982537j

Cited by 158 publications

(233 citation statements)

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“…As shown in Table 5, the DFTcomputed frequencies agree well with our experimental data, correctly predicting the frequency of the ν Fe-N3 mode to be lower for azide 2 than for azide 1 . Additionally, two vibrational modes are predicted at 2063 and 2080 cm −1 that correspond to the in-phase and out-of-phase motions of the two antisymmetric intra-azide stretches (note that both azides contribute almost equally to these two modes).…”

Section: D2 Frequencysupporting

confidence: 79%

“…In this fitting procedure, initial estimates for the Fe-N(azide) and intra-azide force constants were based on values reported for similar complexes. 13,51 The fitted Fe-N(azide) force constants, k Fe-N , of 1.275 and 1.170 mdyne/Å for azide 1 and azide 2 , respectively (Table 5), lie in the range of k Fe-N values reported for similar species. 13,51 Moreover, these values are consistent with the structural parameters obtained by X-ray crystallography, as the Fe-N(azide 1 ) bond is shorter by 0.02 Å than the Fe-N(azide 2 ) bond (Table 4).…”

Section: Ground-state Propertiesmentioning

confidence: 79%

“…The highest-energy occupied azide-based MOs (101b and 103b-105b) are of azide π-nonbonding, π nb , character and oriented either in-plane (ip) or out-of-plane (op) with respect to the Fe-N(azide) plane. The azide 1 π nb -based MOs (101b and 103b) are at lower energy than the azide 2 π nb -based MOs (104b and 105b), and in both cases, the azide π nb (ip)-based MOs (101b and 104b for azide 1 and azide 2 , respectively) are stabilized relative to their respective azide π nb (op)-based MOs (103b and 105b, respectively). Note that the stabilization of the azide 1 π nb -based MOs relative to the azide 2 π nb -based MOs correlates nicely with the difference in the corresponding Fe-N(azide) bond strengths as revealed by our NCA (Table 5).…”

Section: D2 Frequencymentioning

confidence: 94%

“…mp 224-228 °C. 1 [LFeCl] 2 A stirred suspension of HL·2HBr (0.260 g, 0.600 mmol) in tetrahydrofuran (THF) (60 mL) was treated with excess NaH for 2 h. The insoluble material (excess NaH and NaBr) was filtered away and the filtrate evaporated to provide a white solid (NaL). This solid was dissolved in CH 2 Cl 2 (4 mL) and treated with a solution of FeCl 2 (0.080 g, 0.63 mmol) dissolved in CH 3 CN (4 mL).…”

Section: Hl·2hbrmentioning

confidence: 99%

“…SODs can be classified on the basis of the metal ion(s) they require for activity, namely, Mn, Fe, Cu/Zn, or Ni. 1,2 Mn-and FeSODs, like all other SODs, disproportionate the superoxide radical anion into dioxygen and hydrogen peroxide in a two-step ping-pong-type mechanism (eqs 1a and 1b, where M = Fe or Mn) during which the metal ion cycles between the 2+ and 3+ oxidation states. [3][4][5] While structurally unrelated to the Cu/Zn-and NiSODs, Mn-and FeSODs possess nearly identical protein folds and highly homologous active sites.…”

Section: Introductionmentioning

confidence: 99%

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Synthesis, X-Ray Crystallographic Characterization, and Electronic Structure Studies of a Di-Azide Iron(III) Complex: Implications for the Azide Adducts of Iron(III) Superoxide Dismutase

et al. 2008

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We have synthesized and characterized, using X-ray crystallographic, spectroscopic, and computational techniques, a six-coordinate diazide Fe 3+ complex, LFe(N 3 ) 2 (where L is the tetradentate ligand 7-diisopropyl-1,4,7-triazacyclononane-1-acetic acid), that serves as a model of the azide adducts of Fe 3+ superoxide dismutase (Fe 3+ SOD). While previous spectroscopic studies revealed that two distinct azide-bound Fe 3+ SOD species can be obtained at cryogenic temperatures depending on protein and azide concentrations, the number of azide ligands coordinated to the Fe 3+ ion in each species has been the subject of some controversy. In the case of LFe(N 3 ) 2 , the electronic absorption and magnetic circular dichroism spectra are dominated by two broad features centered at 21 500 cm −1 (ε ≈ 4000 M −1 cm −1 ) and ~30 300 cm −1 (ε ≈ 7400 M −1 cm −1 ) attributed to N 3 − → Fe 3+ charge transfer (CT) transitions. A normal coordinate analysis of resonance Raman (RR) data obtained for LFe(N 3 ) 2 indicates that the vibrational features at 363 and 403 cm −1 correspond to the Fe-N 3 stretching modes (ν Fe-N3 ) associated with the two different azide ligands and yields Fe-N 3 force constants of 1.170 and 1.275 mdyne/Å, respectively. RR excitation profile data obtained with laser excitation between 16 000 and 22 000 cm −1 reveal that the ν Fe-N3 modes at 363 and 403 cm −1 are preferentially enhanced upon excitation in resonance with the N 3 − → Fe 3+ CT transitions at lower and higher energies, respectively. Consistent with this result, density functional theory electronic structure calculations predict a larger stabilization of the molecular orbitals of the more strongly bound azide due to increased σ-symmetry orbital overlap with the Fe 3d orbitals, thus yielding higher N 3 − → Fe 3+ CT transition energies. Comparison of our data obtained for LFe(N 3 ) 2 with those reported previously for the two azide adducts of Fe 3+ SOD provides compelling evidence that a single azide is coordinated to the Fe 3+ center in each protein species.© 2008 American Chemical Society * Author to whom correspondence should be addressed. brunold@chem.wisc.edu. Supporting Information Available: Cartesian coordinates of crystal-structure and DFT geometry-optimized LFe(N 3 ) 2 models, INDO/S-CI calculated ZFS parameters for all models of LFe(N 3 ) 2 , DFT predicted MO energies and compositions for LFe(N 3 ) 2 models, TD-DFT calculated electronic excitation energies, Abs and MCD data of LFe(N 3 ) 2 collected at 4.5 K, and analysis of VTVH MCD data collected at 20 661 cm −1 . This material is available free of charge via the Internet at

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Section: D2 Frequencysupporting

confidence: 79%

Section: Ground-state Propertiesmentioning

confidence: 79%

Section: D2 Frequencymentioning

confidence: 94%

Section: Hl·2hbrmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Synthesis, X-Ray Crystallographic Characterization, and Electronic Structure Studies of a Di-Azide Iron(III) Complex: Implications for the Azide Adducts of Iron(III) Superoxide Dismutase

et al. 2008

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Nickel Enzymes & Cofactors

Ragsdale¹

2005

Encyclopedia of Inorganic Chemistry

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This review covers the structure and function of the eight known Ni enzymes, with a focus on the chemistry and biology of the metallocenter. For the Ni redox enzymes, the Ni ion exhibits versatility in redox properties in exploiting the +3/+2 (superoxide dismutase and hydrogenase), the +2/+1 (hydrogenase, CO dehydrogenase, acetyl‐CoA synthase, and methyl‐CoM reductase), and perhaps even reaching the 0 (acetyl‐CoA synthase) states for the redox enzymes. On the other hand, the nonredox Ni enzymes (urease, glyoxylase‐I, aci‐reductone dioxygenase) apparently remain in the +2 state during catalysis. The Ni site(s) in these enzymes adopt a wide variety of coordination environments; some form mononuclear square planar or octahedral complexes, while others are homo‐ or hetero‐ (with iron) dinuclear with oxo or thiolato bridges and still others join heteromultinuclear clusters. Acetyl‐CoA synthase contains the most complex Ni metallocenter yet described, which is a [4Fe–4S] 2+ cluster bridged by a cysteine thiolate to a binuclear NiNi center. The three‐dimensional structures of all these enzymes are known and some (acetyl‐CoA synthase, aci‐reductone dioxygenase, CO dehydrogenase, and superoxide dismutase) have been determined in the past two years leading to a significant reinterpretation of spectroscopic results. In many Ni enzymes, density functional theory has begun to play a major role in assigning active‐site structures and testing mechanistic hypotheses.

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X‐Ray Absorption Spectroscopy

Bencze¹,

Kondapalli²,

Stemmler³

2005

Encyclopedia of Inorganic Chemistry

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X‐ray absorption spectroscopy (XAS), often referred to as X‐ray absorption fine structure (XAFS) spectroscopy, is a powerful technique available for determining the local coordination site structure and electronic properties of specific atoms in molecules. XAS can be performed on molecules in the gaseous, solution, or solid states, and generally every element is spectroscopically active. This technique utilizes high intensity X rays supplied by synchrotron radiation sources to selectively excite core electron transitions for a specific element of choice. XAS spectra are divided into two spectral regions, the X‐ray absorption near edge structure (XANES) region and the extended X‐ray absorption fine structure (EXAFS) region. XANES spectra can be utilized to provide: (1) qualitative information regarding the ligands coordinated to the absorbing atom, (2) semi‐quantitative information regarding the redox state of the absorbing atom, and (3) metal‐ligand coordination geometry. Simulations of the EXAFS data can provide information regarding absorber‐scatterer bond length values to extremely high accuracy (ca. ±0.02 Å), as well as coordination numbers and ligand identity at reduced accuracies. The high accuracy in bond lengths achieved from XAS makes this technique extremely sensitive for measuring subtle structural perturbations within molecules under perturbed or turnover conditions. When utilized with other techniques, XAS can supply the metrical parameters required to understand the chemical properties of specific elements in a molecule.

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Examination of the Nickel Site Structure and Reaction Mechanism in Streptomyces seoulensis Superoxide Dismutase

Cited by 158 publications

References 58 publications

Synthesis, X-Ray Crystallographic Characterization, and Electronic Structure Studies of a Di-Azide Iron(III) Complex: Implications for the Azide Adducts of Iron(III) Superoxide Dismutase

Synthesis, X-Ray Crystallographic Characterization, and Electronic Structure Studies of a Di-Azide Iron(III) Complex: Implications for the Azide Adducts of Iron(III) Superoxide Dismutase

Nickel Enzymes & Cofactors

X‐Ray Absorption Spectroscopy

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