Predicting nitrogen and oxygen kinetic isotope effects of nitrate reduction by periplasmic dissimilatory nitrate reductase

He, Yuyang; Zhang, Yining; Zhang, Siting; Liu, Yun

doi:10.1016/j.gca.2020.10.027

Cited by 9 publications

(12 citation statements)

References 99 publications

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“…The “Best Model” listed comes from the model with 12 explicit H 2 O molecules as well as PCM continuum solvation. The same configuration was selected as the “best” model in a study of NapA isotope fractionation …”

Section: Resultsmentioning

confidence: 99%

“…To test the effect of cluster cutoff sizes on isotope effects, three different sizes of models were created by cutting the ligands on the catalytic Mo atom in different locations. Cut bonds in all active site models are terminated with H atoms; cuts were made at various points in the molybdopterin guanine dinucleotide cofactors, creating models of different sizes . All models had a single Asp amino acid residue ligating the Mo center, with both peptide bonds cut and replaced with H atoms.…”

Section: Methodsmentioning

confidence: 99%

“…The implicit solvation models used are the integral-equation-formalism polarizable continuum model (IEFPCM) or the solvation model density (SMD) model . The initial positions of H 2 O molecules in our NarG models match those from a previous study of the NapA active site, but these positions adjust during model optimization.…”

Section: Methodsmentioning

confidence: 99%

“…The same configuration was selected as the "best" model in a study of NapA isotope fractionation. 33 KIEs are normal for all 15 N and 18 O isotope substitutions on NO 3…”

Section: Models and Vibrational Spectra Of Aqueous Nomentioning

confidence: 98%

“…We link these intrinsic isotope fractionations to variations in δ 15 N, δ 18 O, and 15 ■ METHODS Molecular Modeling. Rhodobacter sphaeroides NapA active site models were obtained from a study of N and O isotope effects 33 which adapted the coordinates of the original protein crystallization (PDB: 1OGY). 54 The structures were modified by the replacement of the Cys residue with a monodentate Asp residue to replicate the active site structure of Escherichia coli NarG enzyme.…”

Section: ■ Introductionmentioning

confidence: 99%

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Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints

Boettger

Neubauer

Kopf

et al. 2022

ACS Earth Space Chem.

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The study of isotopic fingerprints in nitrate (δ15N, δ18O, Δ17O) has enabled pivotal insights into the global nitrogen cycle and revealed new knowledge gaps. Measuring populations of isotopic homologs of intact NO3 – ions (isotopologues) shows promise to advance the understanding of nitrogen cycling processes; however, we need new theory and predictions to guide laboratory experiments and field studies. We investigated the hypothesis that the isotopic composition of the residual nitrate pool is controlled by the N–O bond-breaking step in Nar dissimilatory nitrate reductase using molecular models of the enzyme active sites and associated kinetic isotope effects (KIEs). We integrated the molecular model results into reaction path models representing the reduction of nitrate under either closed-system or steady-state conditions. The predicted intrinsic KIE (15ε and 18ε) of the Nar active site matches observed fractionations in both culture and environmental studies. This is what would be expected if the isotopic composition of marine nitrate were controlled by dissimilatory nitrate reduction by Nar. For a closed system, the molecular models predict a pronounced negative 15N–18O clumping anomaly in residual nitrate. This signal could encode information about the amount of nitrate consumed in a closed system and thus constrain initial nitrate concentration and its isotopic composition. Similar clumped isotope anomalies can potentially be used to distinguish whether a system is open or closed to new nitrate addition. These mechanistic predictions can be tested and refined in combination with emerging ESI-Orbitrap measurements.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…The same configuration was selected as the "best" model in a study of NapA isotope fractionation. 33 KIEs are normal for all 15 N and 18 O isotope substitutions on NO 3…”

Section: Models and Vibrational Spectra Of Aqueous Nomentioning

confidence: 98%

Section: ■ Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints

Boettger

Neubauer

Kopf

et al. 2022

ACS Earth Space Chem.

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Unraveling the mechanism of assimilatory nitrate reduction and methane oxidation by Methylobacter sp. YHQ through dual N-O isotope analysis and kinetic modeling

Chen,

Hao,

Zeng

et al. 2024

Carbon Res.

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Assimilatory nitrate reduction and methane (CH4) oxidation by bacteria play important roles in carbon (C) and nitrogen (N) biogeochemical cycles. Here, an investigation of enzymatic assimilatory nitrate reduction and CH4 oxidation by Methylobacter sp. YHQ from the wetlands is presented, specifically concentrating on N and oxygen (O) isotope fractionation with various initial nitrate and oxygen concentrations. The N enrichment factors (15εassimilation) increased from 4.2 ± 0.7‰ to 6.9 ±1.3‰ and the O isotope enrichment factors (18εassimilation) increased from 2.7 ± 0.9‰ to 4.7 ± 0.8‰ during nitrate assimilation when initial nitrate concentrations increased from 0.9 mM to 2 mM. Similar 18ε and 15ε values were observed at different oxygen concentrations. The values of 18ε and 15ε provided vital parameters for the assessment of assimilatory nitrate reduction via the Rayleigh equation approach. The ratios of O and N isotope enrichment factors (18ε:15ε)assimilation ranged from 0.64 ± 0.15 to 0.74 ± 0.18 during nitrate assimilation by Methylobacter sp. YHQ with Nas, which were different from (18ε:15ε)assimilation for assimilatory eukaryotic nitrate reductase (eukNR) from literature data. Thus, N and O isotope fractionation could be useful tools to distinguish eukNR from Nas during nitrate assimilation. Additionally, the rates of CH4 oxidation and nitrate reduction were evaluated with a reaction-based kinetic model, and it quantitatively described the enzymatic reactions of nitrate assimilation. Combining dual N-O isotope analysis with kinetic modeling provides new insights into the microbially driven C-N interactions. Graphical Abstract

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Density functional theory calculations of nitrogen and oxygen equilibrium isotope fractionations in NO3−–NO2−–H2O aqueous system reveal inverse kinetic isotope effects during nitrite oxidation

2022

Applied Geochemistry

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Predicting nitrogen and oxygen kinetic isotope effects of nitrate reduction by periplasmic dissimilatory nitrate reductase

Cited by 9 publications

References 99 publications

Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints

Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints

Unraveling the mechanism of assimilatory nitrate reduction and methane oxidation by Methylobacter sp. YHQ through dual N-O isotope analysis and kinetic modeling

Density functional theory calculations of nitrogen and oxygen equilibrium isotope fractionations in NO3−–NO2−–H2O aqueous system reveal inverse kinetic isotope effects during nitrite oxidation

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