Unique Binding of Nitric Oxide to Ferric Nitric Oxide Reductase from <i>Fusarium oxysporum</i> Elucidated with Infrared, Resonance Raman, and X-ray Absorption Spectroscopies

Obayashi, E.; Tsukamoto, Keizou; Adachi, Shin‐ichi; Takahashi, Satoshi; Nomura, Masaharu; Iizuka, Tetsutarō; Shoun, Hirofumi; Shiro, Yoshitsugu

doi:10.1021/ja9637816

Cited by 102 publications

(124 citation statements)

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“…Bond lengths from the EXAFS studies of CYP119 and its derivatives are listed in Table 2, which also contains previously reported EXAFS results for porphyrin-iron-oxo species (17,(36)(37)(38)(39)(40)(41) and heme-thiolate nitrosyl complexes (42). We note that the errors in EXAFS bond lengths typically are 0.01-0.02 Å.…”

Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

“…The corresponding bond length in the nitrosyl complex of the hemethiolate nitric oxide reductase enzyme (P450 nor ) is 1.66 Å (42), and x-ray crystallographic studies of a model porphyrin nitrosyl derivative with a trans-thiolate ligand gave an iron-nitrogen bond length of 1.67 Å (51). The CYP119-NO result is, however, similar to that for the P450 cam -NO complex, which has a 1.76-Å ironnitrogen bond (42). A long iron-nitrogen (nitrosyl) bond length for CYP119-NO implies a significantly bent Fe-N-O bond, which is consistent with our inability to isolate multiple scattering from the nitrosyl oxygen atom (52).…”

Section: Resultsmentioning

confidence: 99%

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X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative

Newcomb

Halgrimson

Horner

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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The cytochrome P450 enzyme CYP119, its compound II derivative, and its nitrosyl complex were studied by iron K-edge x-ray absorption spectroscopy. The compound II derivative was prepared by reaction of the resting enzyme with peroxynitrite and had a lifetime of Ϸ10 s at 23°C. The CYP119 nitrosyl complex was prepared by reaction of the enzyme with nitrogen monoxide gas or with a nitrosyl donor and was stable at 23°C for hours. Samples of CYP119 and its derivatives were studied by x-ray absorption spectroscopy at temperatures below 140 (K) at the Advanced Photon Source of Argonne National Laboratory. The x-ray absorption near-edge structure spectra displayed shifts in edge and pre-edge energies consistent with increasing effective positive charge on iron in the series native CYP119 < CYP119 nitrosyl complex < CYP119 compound II derivative. Extended x-ray absorption fine structure spectra were simulated with good fits for k ‫؍‬ 12 Å ؊1 for native CYP119 and k ‫؍‬ 13 Å ؊1 for both the nitrosyl complex and the compound II derivative. The important structural features for the compound II derivative were an iron-oxygen bond length of 1.82 Å and an iron-sulfur bond length of 2.24 Å, both of which indicate an iron-oxygen single bond in a ferryl-hydroxide, Fe IV OH, moiety.EXAFS ͉ ferryl-oxo ͉ XANES

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Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative

Newcomb

Halgrimson

Horner

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…We have searched in the 1800 -2000 cm Ϫ1 RR range and found no evidence for such a mode in our Soret excitation data, in agreement with previous observations in other His-Fe-NO complexes. The stretching frequency of Fe 3ϩ -NO in P-450, which has cysteine as the proximal ligand, is about 70 cm Ϫ1 downshifted compared with that of heme proteins possessing histidine as the proximal ligand (15,16,18). Variations in the basicity of the proximal ligand are likely to contribute to the vibrational differences between the cysteine-and histidinecontaining ferric nitrosyl complexes.…”

Section: Structures Of Oxidized Reduced and No-bound Forms In Normentioning

confidence: 96%

“…This observation was attributed to the little orbital conjugation that exists between the NO group and the heme in the His-Fe-NO complexes. In the cysteinecontaining enzyme P-450Nor, however, in addition to the Fe-NO stretching vibration, the N-O has been detected using Soret excitation (18). Recently, the (NO) of His-Fe 3ϩ -NO heme proteins was reported by applying UV RR excitation (15).…”

Section: Structures Of Oxidized Reduced and No-bound Forms In Normentioning

confidence: 99%

Nitric-oxide Reductase

Pinakoulaki¹,

Gemeinhardt²,

Saraste³

et al. 2002

Journal of Biological Chemistry

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We have applied resonance Raman spectroscopy to investigate the properties of the dinuclear center of oxidized, reduced, and NO-bound nitric-oxide reductase from Paracoccus denitrificans. , respectively. The nitrosyl species we detect is photolabile and can be photolyzed to generate a new form of oxidized enzyme in which the proximal histidine is ligated to heme b 3 , in contrast to the resting form. Photodissociation of the NO ligand yields a five-coordinate high-spin heme b 3 . Based on the findings reported here, the structure and properties of the dinuclear center of nitricoxide reductase in the oxidized, reduced, and NO-bound form as well as its photoproduct can be described with certainty.The bacterial nitric-oxide reductase (Nor) 1 complex forms the N-N bond during denitrification (1-4). It is a membrane-bound cytochrome bc complex composed of two subunits, NorC and NorB, that catalyzes the reduction of NO to N 2 O (5). The complex contains four known redox centers: three heme groups and one non-heme Fe atom (5-7). Heme c (six-coordinate, lowspin) is bound to NorC subunit and functions as the electron entry site of the enzyme. NorB contains one six-coordinate, low-spin heme b and a five-coordinate, high-spin heme b 3 , which, together with a non-heme iron atom, form the dinuclear NO reduction site. The sequence of NorB contains all six histidines that are the ligands of heme a, heme a 3 , and Cu B in cytochrome c oxidase (4).Resonance Raman (RR) scattering is a powerful technique for the study of heme proteins because the spectra are rich in information about the heme groups (8, 9). Moreover, vibrational modes of ligands bound to heme may be assigned by isotopic substitution measurements, and their properties, which reflect ligand structure, may be studied. It has been reported that in oxidized Nor, heme b 3 is not coordinated to the protein by its proximal histidine residue (6). In addition, the single oxygen isotope-sensitive ligand vibration observed at 811 cm Ϫ1 in the RR spectrum was attributed to the as (Fe-OFe) of the heme b 3 /non-heme diiron center (7). However, the structural implications involved in the transition from oxidized to reduced enzyme were not reported.The properties of oxidized Nor, when compared with those of the chemically generated deoxy (five-coordinate) and the nitrosyl complex, can be related to structural changes that take place in the protein upon ligand binding and release. It is these interactions between the heme and the protein that determine the biological properties of the heme protein. Moreover, in unraveling the NO protonation mechanism, it is necessary to establish sites in the enzyme that have exchangeable protons. If there are such sites near the high-spin heme b 3 or the non-heme Fe, then solvent exchange from protonated to deuterated buffers could lead to changes in the RR spectra because the vibrational frequencies are sensitive to effective mass.In an effort to gain information concerning these observations, we have used 413.1 nm RR excitation to examine the s...

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Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy

2000

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An overview of the application of Fourier transform infrared spectroscopy for the analysis of the structure of proteins and protein–ligand recognition is given. The principle of the technique and of the spectra analysis is demonstrated. Spectral signal assignments to vibrational modes of the peptide chromophore, amino acid side chains, cofactors and metal ligands are summarized. Several examples for protein–ligand recognition are discussed. A particular focus is heme proteins and, as an example, studies of cytochrome P450 are reviewed. Fourier transform infrared spectroscopy in combination with the various techniques such as time‐resolved and low‐temperature methods, site‐directed mutagenesis and isotope labeling is a helpful approach to studying protein–ligand recognition. Copyright © 2000 John Wiley & Sons, Ltd.

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Unique Binding of Nitric Oxide to Ferric Nitric Oxide Reductase from Fusarium oxysporum Elucidated with Infrared, Resonance Raman, and X-ray Absorption Spectroscopies

Cited by 102 publications

References 36 publications

X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative

X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative

Nitric-oxide Reductase

Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy

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