A new structural insight into differential interaction of cyanobacterial and plant ferredoxins with nitrite reductase as revealed by NMR and X-ray crystallographic studies

Sakakibara, Yukiko; Kimura, Hitoshi; Iwamura, Akira; Saitoh, Takashi; Kurisu, Genji; Hase, Toshiharu

doi:10.1093/jb/mvs028

Cited by 32 publications

(33 citation statements)

References 34 publications

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“…The initial step of nitrate assimilation, the conversion of nitrate to nitrite, is catalyzed by nitrate reductase in the cytosol, using NAD(P)H as a reducing power. The highly reactive nitrite is immediately transported into the plastid, where it is converted to ammonium by nitrite reductase (NiR) using Fdx as an electron donor (144,297). Eight molecules of reduced Fdx are required to reduce one molecule of nitrate to ammonium.…”

Section: Lipid Synthesismentioning

confidence: 99%

Metabolic Control of Redox and Redox Control of Metabolism in Plants

Geigenberger

Fernie

2014

Antioxidants & Redox Signaling

139

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Significance: Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. Recent Advances: The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. Critical Issues: It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter-and intracellular levels. Future Directions: Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.

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Section: Lipid Synthesismentioning

confidence: 99%

Metabolic Control of Redox and Redox Control of Metabolism in Plants

Geigenberger

Fernie

2014

Antioxidants & Redox Signaling

139

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“…Detailed studies on enzyme activities and electron transfer rates based on the static and dynamic structures determined by X-ray crystallography and solution NMR spectroscopy have increased our understanding of the molecular mechanisms underlying electron flow and enzymatic activities in photosynthesis and respiration [3,[9][10][11][12]. Solution NMR spectroscopy and calorimetry have provided further information on the dynamic structures of proteins and molecular origins of intermolecular interactions for protein functions [3,13].…”

Section: Introductionmentioning

confidence: 99%

“…Fd is considered to be a good model protein because it transfers an electron obtained from photosystem I to several target enzymes, including ferredoxin-NADP + reductase (FNR), sulfite reductase (SiR), nitrite reductase (NiR), and hydrogenase [17], through the formation of electron transfer protein complexes [9,11,18]. Fd is a small acidic protein (~10.5 kDa) that accommodates the redox center of the [2Fe-2S] cluster [5].…”

Section: Introductionmentioning

confidence: 99%

“…These findings indicated the contribution of hydrophobic interactions, which have received less attention than electrostatic contributions, to FNR activity. The strong potential for charge clusters on the surfaces of electron transfer proteins [25,27] and NMR invisible hydrophobic regions of Fd due to paramagnetic relaxation enhancements from the unpaired electrons of iron [9] may have led to the biased interpretation of electrostatic interactions by masking hydrophobic contributions.…”

Section: Introductionmentioning

confidence: 99%

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Physicochemical nature of interfaces controlling ferredoxin NADP+ reductase activity through its interprotein interactions with ferredoxin

Kinoshita

Kim

Kume³

et al. 2015

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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Although acidic residues of ferredoxin (Fd) are known to be essential for activities of various Fd-dependent enzymes, including ferredoxin NADP(+) reductase (FNR) and sulfite reductase (SiR), through electrostatic interactions with basic residues of partner enzymes, non-electrostatic contributions such as hydrophobic forces remain largely unknown. We herein demonstrated that intermolecular hydrophobic and charge-charge interactions between Fd and enzymes were both critical for enzymatic activity. Systematic site-directed mutagenesis, which altered physicochemical properties of residues on the interfaces of Fd for FNR /SiR, revealed various changes in activities of both enzymes. The replacement of serine 43 of Fd to a hydrophobic residue (S43W) and charged residue (S43D) increased and decreased FNR activity, respectively, while S43W showed significantly lower SiR activity without affecting SiR activity by S43D, suggesting that hydrophobic and electrostatic interprotein forces affected FNR activity. Enzyme kinetics revealed that changes in FNR activity by mutating Fd correlated with Km, but not with kcat or activation energy, indicating that interprotein interactions determined FNR activity. Calorimetry-based binding thermodynamics between Fd and FNR showed different binding modes of FNR to wild-type, S43W, or S43D, which were controlled by enthalpy and entropy, as shown by the driving force plot. Residue-based NMR spectroscopy of (15)N FNR with Fds also revealed distinct binding modes of each complex based on different directions of NMR peak shifts with similar overall chemical shift differences. We proposed that subtle adjustments in both hydrophobic and electrostatic forces were critical for enzymatic activity, and these results may be applicable to protein-based electron transfer systems.

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“…For PetF from different organisms, the bindingi nterface with nitrite reductase, [12] ferredoxin NADP + oxidoreductase…”

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confidence: 99%

Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase from Chlamydomonas reinhardtii

et al. 2015

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The transfer of photosynthetic electrons by the ferredoxin PetF to the [FeFe] hydrogenase HydA1 in the microalga Chlamydomonas reinhardtii is a key step in hydrogen production. Electron delivery requires a specific interaction between PetF and HydA1. However, because of the transient nature of the electron-transfer complex, a crystal structure remains elusive. Therefore, we performed protein-protein docking based on new experimental data from a solution NMR spectroscopy investigation of native and gallium-substituted PetF. This provides valuable information about residues crucial for complex formation and electron transfer. The derived complex model might help to pinpoint residue substitution targets for improved hydrogen production.

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A new structural insight into differential interaction of cyanobacterial and plant ferredoxins with nitrite reductase as revealed by NMR and X-ray crystallographic studies

Cited by 32 publications

References 34 publications

Metabolic Control of Redox and Redox Control of Metabolism in Plants

Metabolic Control of Redox and Redox Control of Metabolism in Plants

Physicochemical nature of interfaces controlling ferredoxin NADP+ reductase activity through its interprotein interactions with ferredoxin

Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase from Chlamydomonas reinhardtii

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