The molecular structure of the high potential iron-sulfur protein isolated from Ectothiorhodospira halophila determined at 2.5-A resolution.

Breiter, Deborah R.; Meyer, Terrance E.; Rayment, Ivan; Holden, Hazel M.

doi:10.1016/s0021-9258(18)55114-0

Cited by 90 publications

(39 citation statements)

References 29 publications

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“…[4Fe–4S] ferredoxins were studied from Bacillus thermoproteolyticus (1IQZ; 4Fd1), 42 Desulfovibrio africanus (1FXR; 4Fd2), 43 and A. vinelandii (5FD1; 4Fd3) 41 with differences in the potential of 370 mV. Finally, HiPIP sites were studied from Allochromatium vinosum (1CKU; Hip1) 47 and Halorhodospira halophila (2HIP; Hip2), 46 with a difference in the potential of 235 mV. In total, the considered redox potentials cover a range of 1005 mV from −650 to 355 mV.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, each Fe ion also coordinates to a Cys residue. 44 They employ the Fe 3 II Fe 1 III /Fe 2 II Fe 2 III redox couple, giving redox potentials of −0.7 to −0.3 V. 45 The high-potential iron proteins (HiPIP) have the same cubane structure, 46 , 47 but they use instead the Fe 2 II Fe 2 III /Fe 1 II Fe 3 III redox couple, giving them a much more positive potential (+0.05 to +0.5 V). 45 Finally, the [3Fe–4S] ferredoxins have a distorted cubane structure, in which one Fe ion and one Cys residue are missing.…”

Section: Introductionmentioning

confidence: 99%

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Benchmark Study of Redox Potential Calculations for Iron–Sulfur Clusters in Proteins

et al. 2022

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Redox potentials have been calculated for 12 different iron–sulfur sites of 6 different types with 1–4 iron ions. Structures were optimized with combined quantum mechanical and molecular mechanical (QM/MM) methods, and the redox potentials were calculated using the QM/MM energies, single-point QM methods in a continuum solvent or by QM/MM thermodynamic cycle perturbations. We show that the best results are obtained with a large QM system (∼300 atoms, but a smaller QM system, ∼150 atoms, can be used for the QM/MM geometry optimization) and a large value of the dielectric constant (80). For absolute redox potentials, the B3LYP density functional method gives better results than TPSS, and the results are improved with a larger basis set. However, for relative redox potentials, the opposite is true. The results are insensitive to the force field (charges of the surroundings) used for the QM/MM calculations or whether the protein and solvent outside the QM system are relaxed or kept fixed at the crystal structure. With the best approach for relative potentials, mean absolute and maximum deviations of 0.17 and 0.44 V, respectively, are obtained after removing a systematic error of −0.55 V. Such an approach can be used to identify the correct oxidation states involved in a certain redox reaction.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Benchmark Study of Redox Potential Calculations for Iron–Sulfur Clusters in Proteins

et al. 2022

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“…In its oxidized form, it formally contains one Fe 2+ ion and three Fe 3+ ions, but experimental data are consistent with the cluster being formed by one mixed-valence pair (with S = 9/2), containing two Fe 2.5+ ions and one ferric ions pair containing two Fe 3+ ions (forced by exchange coupling to S = 4, see later), resulting in an overall spin of the cluster equal to 1/2. 20,21 Over the past 20 years, EhHiPIP I has become a model system for biophysical applications, and it has been extensively characterized by X-ray crystallography, 22 electron paramagnetic resonance (EPR) and Mossbauer measurements at very low temperatures, 23 Raman spectroscopy, 23 and solution NMR, 21,24 where the electronic properties of the Fe 4 S 4 cluster give distinctive features in the 1 H 24,25 and 13 C spectra. 21 The electronic properties of Fe 4 S 4 clusters are made extremely complex by the presence of the highly asymmetric protein matrix that induces equilibria between different charge distributions among the iron ions.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Over the past 20 years, Eh HiPIP I has become a model system for biophysical applications, and it has been extensively characterized by X-ray crystallography, electron paramagnetic resonance (EPR) and Mössbauer measurements at very low temperatures, Raman spectroscopy, and solution NMR, , where the electronic properties of the Fe 4 S 4 cluster give distinctive features in the 1 H , and 13 C spectra . The electronic properties of Fe 4 S 4 clusters are made extremely complex by the presence of the highly asymmetric protein matrix that induces equilibria between different charge distributions among the iron ions.…”

Section: Introductionmentioning

confidence: 99%

“…Most notably here, the unit cell of crystalline Eh HiPIP I contains two molecules, featuring an overall backbone RMSD of 0.67 Å (Figure ). Considering that paramagnetic NMR shifts are highly sensitive to the local geometry, solid-state NMR could be able to capture distinct signatures from the two conformations present in the asymmetric unit.…”

Section: Introductionmentioning

confidence: 99%

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Paramagnetic Properties of a Crystalline Iron–Sulfur Protein by Magic-Angle Spinning NMR Spectroscopy

et al. 2017

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We present the first solid-state NMR study of an iron-sulfur protein. The combined use of very fast (60 kHz) magic-angle spinning and tailored radiofrequency irradiation schemes allows the detection and the assignment of most of the H andC resonances of the oxidized high-potential iron-sulfur protein I from Ectothiorhodospira halophila (EhHiPIP I), including those in residues coordinating the FeS cluster. For these residues, contact shifts as large as 100 and 400 ppm for H andC resonances, respectively, were observed, which represent the most shifted solid-state NMR signals ever measured in metalloproteins. Interestingly, by targeting EhHiPIP I in a crystalline environment, we were able to capture distinct paramagnetic signatures from the two conformations present in the asymmetric unit. The magnetic properties of the system were verified by following the temperature dependence of the contact-shifted cysteine resonances.

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Topological chirality of iron-sulfur proteins

Liang

Mislow

1997

Biopolymers

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An examination of x‐ray structures of single‐cluster [4Fe‐4S] proteins in the Protein Data Bank has revealed that all redox proteins and the glutamine 5‐phosphoribosyl‐1‐pyrophosphate amidotransferase from Bacillus subtilis have a topological configuration arbitrarily designated as D, whereas the DNA repair enzyme endonuclease III from Escherichia coli has the opposite topological configuration, L. This is the first example in which both senses of topological chirality have been observed in a class of proteins. © 1997 John Wiley & Sons, Inc. Biopoly 42: 411–414, 1997

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The molecular structure of the high potential iron-sulfur protein isolated from Ectothiorhodospira halophila determined at 2.5-A resolution.

Cited by 90 publications

References 29 publications

Benchmark Study of Redox Potential Calculations for Iron–Sulfur Clusters in Proteins

Benchmark Study of Redox Potential Calculations for Iron–Sulfur Clusters in Proteins

Paramagnetic Properties of a Crystalline Iron–Sulfur Protein by Magic-Angle Spinning NMR Spectroscopy

Topological chirality of iron-sulfur proteins

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