A5037062657- Hemoglobin structure and function
- Photosynthetic Processes and Mechanisms
- Metal-Catalyzed Oxygenation Mechanisms
- Pharmacogenetics and Drug Metabolism
- Heme Oxygenase-1 and Carbon Monoxide
- Nitric Oxide and Endothelin Effects
- Porphyrin Metabolism and Disorders
- Porphyrin and Phthalocyanine Chemistry
- Mass Spectrometry Techniques and Applications
- Enzyme Structure and Function
- Tryptophan and brain disorders
- Neonatal Health and Biochemistry
- Photoreceptor and optogenetics research
- Erythrocyte Function and Pathophysiology
- Microbial Fuel Cells and Bioremediation
- Protein Structure and Dynamics
- Electron Spin Resonance Studies
- Chemical Reactions and Isotopes
- Bacterial Genetics and Biotechnology
- Computational Drug Discovery Methods
- Cancer Treatment and Pharmacology
- Electrochemical sensors and biosensors
- Mitochondrial Function and Pathology
- Redox biology and oxidative stress
- Analytical Chemistry and Chromatography
University of Hyogo
2016-2025
Yamaguchi University
2024
SPring-8
2011-2022
Japan Synchrotron Radiation Research Institute
2018
RIKEN
2000-2015
Hokkaido University
2014
Hyogo University
2014
In-Q-Tel
2013
Quantum Chemistry Research Institute
2010
Osaka University
2001-2010
Human indoleamine 2,3-dioxygenase (IDO) catalyzes the cleavage of pyrrol ring l -Trp and incorporates both atoms a molecule oxygen (O 2 ). Here we report on x-ray crystal structure human IDO, complexed with ligand inhibitor 4-phenylimidazole cyanide. The overall IDO shows two α-helical domains heme between them. A264 flexible loop in distal side is close proximity to iron. A mutant analysis that none polar amino acid residues pocket are essential for activity, suggesting that, unlike...
Dissecting Nitric Oxide Reductase Bacterial breakdown of nitrogen compounds in soil and the oceans provides largest emission source greenhouse gas, nitrous oxide (N 2 O). A key enzyme this process is nitric reductase (NOR), which catalyzes reduction (NO) to N O. Hino et al. (p. 1666 , published online 25 November; see Perspective by Moënne-Loccoz Fee ) now describe crystal structure NOR from Pseudomonas aeruginosa . Consistent with their evolutionary relatedness, transmembrane region...
Cytochrome P450 isolated from Bacillus subtilis (P450(BSbeta); molecular mass, 48 kDa) catalyzes the hydroxylation of a long-chain fatty acid (e.g. myristic acid) at alpha- and beta-positions using hydrogen peroxide as an oxidant. We report here on crystal structure ferric P450(BSbeta) in substrate-bound form, determined resolution 2.1 A. exhibits typical fold. The substrate binds to specific channel enzyme is stabilized through hydrophobic interactions its alkyl side chain with some...
The structural basis for the photochromism in fluorescent protein Dronpa is poorly understood, because crystal structures of bright state did not provide an answer to mechanism photochromism, and determination dark has been elusive. We performed NMR analyses solution at ambient temperatures find flexibility state. Light-induced changes interactions between chromophore β-barrel are responsible switching two states. In state, apex tethers barrel by a hydrogen bond, imidazole ring protruding...
Cytochrome P450(SPα) (CYP152B1) isolated from Sphingomonas paucimobilis is the first P450 to be classified as a H(2)O(2)-dependent P450. hydroxylates fatty acids with high α-regioselectivity. Herein we report crystal structure of palmitic acid substrate at resolution 1.65 Å. The revealed that C(α) bound in one alternative conformations 4.5 Å heme iron. This conformation explains highly selective α-hydroxylation observed P450(SPα). Mutations active site and F-G loop did not impair its...
Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers crystallographic method to track enzymatic reactions. Here we demonstrate the application of this fungal NO reductase, heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, identify NO-bound form which is initial intermediate slightly bent Fe-N-O coordination geometry resolution 2.1 Å. The compatible those...
Trick or treat: Cytochrome P450BSβ was transformed into a monooxygenase suitable for practical use by employing simple substrate trick. The specificity of altered drastically decoy molecule, while its intrinsic advantage, the hydrogen peroxide, retained. catalytic activities and enantioselectivity H2O2–P450BSβ system are highly dependent on structure molecule. Supporting information this article is available WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z700068_s.pdf from author....
The endogenous calcium ion (Ca"') in horseradish peroxidase (HRP) was removed to cause substantial changes the proton NMR spectra of enzyme various OxidationJspin states.The spectral were interpreted as arising from alterations heme environments, most likely proximal and distal sides.The comparative kinetic redox studies revealed that these conformational affect reduction process compound 11, resulting decrease enzymatic activity HRP.It is also ESR spectrum temperature dependences optical...
Staurosporine isolated from Streptomyces sp. TP-A0274 is a member of the family indolocarbazole alkaloids that exhibit strong antitumor activity. A key step in staurosporine biosynthesis formation core by intramolecular C-C bond and oxidative decarboxylation chromopyrrolic acid (CPA) catalyzed cytochrome P450 StaP (StaP, CYP245A1). In this study, we report x-ray crystal structures CPA-bound -free forms StaP. Upon substrate binding, adopts more ordered conformation, conformational...
Unique heme-containing tryptophan 2,3-dioxygenase (TDO) and indoleamine (IDO) catalyze oxidative cleavage of the pyrrole ring l-tryptophan (Trp). Although these two heme dioxygenases were discovered more than 40 years ago, their reaction mechanisms still poorly understood. Encouraged by recent X-ray crystal structures, new mechanistic pathways proposed. We performed ONIOM(B3LYP:Amber) calculations with explicit consideration protein environment to study various possible for bacterial TDO....
The direct hydroxylation of alkanes under mild conditions is a key issue in catalytic chemistry that addresses an increasing number industrial and economic requirements. Cytochrome P450s are monooxygenases capable oxidizing less reactive C–H bonds; however, wild-type unavailable for many important nonnative substrates such as gaseous alkanes. Here, we report the enhanced activities crystallographic evidence role decoy molecules P450BM3-catalyzed ethane propane by using next generation...
The selective hydroxylation of benzene to phenol, without the formation side products resulting from overoxidation, is catalyzed by cytochrome P450BM3 with assistance amino acid derivatives as decoy molecules. catalytic turnover rate and total number reached 259 min-1 P450BM3-1 40 200 when N-heptyl-l-proline modified l-phenylalanine (C7-l-Pro-l-Phe) was used molecule. This work shows that a totally different structure fatty acids can be molecules for aromatic wild-type P450BM3. method...
A mechanistic study of H2O2-dependent C-H bond hydroxylation by myoglobin reconstituted with a manganese porphycene was carried out. The X-ray crystal structure the protein obtained at 1.5 Å resolution reveals tight incorporation complex into matrix pH 8.5, optimized value for highest turnover number ethylbenzene. generates spectroscopically detectable two-electron oxidative intermediate in reaction peracid, which has half-life up to 38 s 10 °C. Electron paramagnetic resonance spectra...
Nitric-oxide reductase (NOR) of a denitrifying bacterium catalyzes NO reduction to N(2)O at the binuclear catalytic center consisting high spin heme b(3) and non-heme Fe(B). The structures reaction intermediates in single turnover by NOR from Pseudomonas aeruginosa were investigated using optical absorption EPR spectroscopies combined with an originally designed freeze-quench device. In spectrum sample, which fully reduced was mixed solution quenched 0.5 ms after mixing, two characteristic...
Nitric oxide reductase from the denitrifying fungus Fusarium oxysporum catalyzes reduction of NO to N2O [Nakahara, K., et al. J. Biol. Chem. 1993, 268, 8350−8355]. Since this enzyme belongs cytochrome P450 superfamily [Kizawa, H., 1991, 266, 10632−10637], it is called P450nor (P450nor), but does not exhibit monooxygenation activity. In present study, we examine coordination structure heme iron in ferric-NO form by using infrared, resonance Raman, and X-ray absorption (EXAFS = extended fine...
Fungal nitric-oxide reductase (NOR) is a heme enzyme that catalyzes the reduction of NO to N<sub>2</sub>O through its ferric-NO complex, first intermediate catalysis. Crystal structures forms wild type (WT) fungal NOR, and Ser<sup>286</sup> → Val Thr mutant enzymes were determined 1.7-Å resolution at cryogenic temperature (100 K). This shows slightly tilted bent binding iron, in sharp contrast highly coordination found ferrous hemoproteins. In WT structure, specific hydrogen-bonding network...