Dataset Information

Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism.

ABSTRACT: 3-mercaptopropionate (3MPA) dioxygenase (MDO) is a mononuclear nonheme iron enzyme that catalyzes the O₂-dependent oxidation of thiol-bearing substrates to yield the corresponding sulfinic acid. MDO is a member of the cysteine dioxygenase family of small molecule thiol dioxygenases and thus shares a conserved sequence of active site residues (Serine-155, Histidine-157, and Tyrosine-159), collectively referred to as the SHY-motif. It has been demonstrated that these amino acids directly interact with the mononuclear Fe-site, influencing steady-state catalysis, catalytic efficiency, O₂-binding, and substrate coordination. However, the underlying mechanism by which this is accomplished is poorly understood. Here, pulsed electron paramagnetic resonance spectroscopy [¹H Mims electron nuclear double resonance) spectroscopy] is applied to validate density functional theory computational models for the MDO Fe-site simultaneously coordinated by substrate and nitric oxide (NO), (3MPA/NO)-MDO. The enhanced resolution provided by electron nuclear double resonance spectroscopy allows for direct observation of Fe-bound substrate conformations and H-bond donation from Tyr159 to the Fe-bound NO ligand. Further inclusion of SHY-motif residues within the validated model reveals a distinct channel restricting movement of the Fe-bound NO-ligand. It has been argued that the iron-nitrosyl emulates the structure of potential Fe(III)-superoxide intermediates within the MDO catalytic cycle. While the merit of this assumption remains unconfirmed, the model reported here offers a framework to evaluate oxygen binding at the substrate-bound Fe-site and possible reaction mechanisms. It also underscores the significance of hydrogen bonding interactions within the enzymatic active site.

SUBMITTER: Pierce BS

PROVIDER: S-EPMC10966181 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism.

Pierce Brad S BS Schmittou Allison N AN York Nicholas J NJ Madigan Ryan P RP Nino Paula F PF Foss Frank W FW Lockart Molly M MM

The Journal of biological chemistry 20240221 4

3-mercaptopropionate (3MPA) dioxygenase (MDO) is a mononuclear nonheme iron enzyme that catalyzes the O<sub>2</sub>-dependent oxidation of thiol-bearing substrates to yield the corresponding sulfinic acid. MDO is a member of the cysteine dioxygenase family of small molecule thiol dioxygenases and thus shares a conserved sequence of active site residues (Serine-155, Histidine-157, and Tyrosine-159), collectively referred to as the SHY-motif. It has been demonstrated that these amino acids directl ...[more]

PMID: 38395308

Similar Datasets

Project description:Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur nonrandomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. Here, ribosomal DNA amplicon sequencing from grape musts and RNA sequencing of eukaryotic transcripts from primary fermentations inoculated with the wine yeast Saccharomyces cerevisiae RC212 were used to profile fermentations from 15 vineyards in California and Oregon across two vintages. These data demonstrate that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing correlated with neither transcript abundance from those same organisms within the RNA sequencing data nor gene expression of the inoculated RC212 yeast strain. These data suggest that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing were not active during the primary stage of these inoculated fermentations and were not a major factor in determining RC212 gene expression. However, unique genetic signatures were detected within the ribosomal DNA amplicon and eukaryotic transcriptomic sequencing that were predictive of vineyard site and region. These signatures included S. cerevisiae gene expression patterns linked to nitrogen, sulfur, and thiamine metabolism. These genetic signatures of site offer insight into specific environmental factors to consider with respect to fermentation outcomes and vineyard site and regional wine characteristics.IMPORTANCE The wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. In this work, as in previous studies, it is demonstrated that specific bacteria and fungi are associated with individual wine regions and vineyard sites. However, this work further shows that their presence is not associated with detectable fungal gene expression during the primary fermentation or the expression of specific genes by the inoculate Saccharomyces cerevisiae strain RC212. The detected RC212 gene expression signatures associated with region and vineyard site also allowed the identification of flavor-associated metabolic processes and environmental factors that could impact primary fermentation outcomes. These data offer novel insights into the complexities and subtleties of vineyard-specific inoculated wine fermentation and starting points for future investigations into factors that contribute to regional wine distinctiveness.

Project description:Carotenoids are indispensable molecules for life. They are present everywhere in plants, algae, bacteria whom they protect against free radicals and oxidative stress. Through the consumption of fruits and vegetables and some carotenoid-containing fish, they are introduced into the human body and, similarly, protect it. There are numerous health benefits associated with the consumption of carotenoids. Carotenoids are antioxidants but at the same time they are prone to oxidation themselves. Electron loss from the carotenoid forms a radical cation. Furthermore, proton loss from a radical cation forms a neutral radical. In this mini-review, we discuss carotenoid radicals studied in our groups by various physicochemical methods, namely the radical cations formed by electron transfer and neutral radicals formed by proton loss from the radical cations. They contain many similar hyperfine couplings due to interactions between the electron spin and numerous protons in the carotenoid. Different EPR and ENDOR methods in combination with DFT calculations have been used to distinguish the two independent carotenoid radical species. DFT predicted larger coupling constants for the neutral radical compared to the radical cation. Previously, INDO calculations miss assigned the large couplings to the radical cation. EPR and ENDOR have aided in elucidating the physisorb, electron and proton transfer processes that occur when carotenoids are adsorbed on solid artificial matrices, and predicted similar reactions in aqueous solution or in plants. After years of study of the physicochemical properties of carotenoid radicals, the different published results start to merge together for a better understanding of carotenoid radical species and their implication in biological systems. Up until 2008, the radical chemistry in artificial systems was elucidated but the correlation between quenching ability and neutral radical formation was an inspiration to look for these radical species in vivo. In addition, the EPR spin-trapping technique has been applied to study inclusion complexes of carotenoids with different delivery systems.

Dataset Information

Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism.

Publications

Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets