Insights into unknown foreign ligand in copper nitrite reductase

Fukuda, Youichi; Tse, K.M.; Kado, Yuji; Mizohata, Eiichi; Matsumura, Hideki; Inoue, Tsuyoshi

doi:10.1016/j.bbrc.2015.07.025

Cited by 8 publications

(14 citation statements)

References 36 publications

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“…The appearance of the oxygen ligand is more significant owing to the novel binding mode exhibited in comparison to previously described structures with bound diatomic molecules ( Fig. 5a; Antonyuk et al, 2005;Fukuda et al, 2015). Here, we observe a mononuclear copper(II)-superoxo complex with asymmetric O-O binding.…”

Section: Comparison Of Srx Rs and Sf-rox Structuressupporting

confidence: 66%

“…Here, we observe a mononuclear copper(II)-superoxo complex with asymmetric O-O binding. This differs from the O 2 binding observed in GtNiR, where the binding is relatively symmetric, and is more similar to NO binding after NO 2 À reduction in AcNiR, with O distal and O proximal bond distances of 2.40 and 2.13 Å , respectively, as opposed to 2.65 and 1.81 Å in AxNiR (Antonyuk et al, 2005;Fukuda et al, 2015). This shift may be owing to the replacement of isoleucine with valine in GtNiR, a thermophilic protein, that creates great steric hindrance to the ligand.…”

Section: Comparison Of Srx Rs and Sf-rox Structuresmentioning

confidence: 63%

“…However, despite the determination of numerous structures of AxNiR using synchrotron radiation from cryogenically maintained crystals, O 2 bound to the T2Cu has never been observed. In a recent X-ray spectroscopic study of the oxidase-positive NiR from Geobacillus thermodenitrificans (GtNiR), radiation-induced chemistry was associated with the observation of a diatomic ligand, suggested to be side-on-bound dioxygen (Fukuda et al, 2015). Detection of this species has been suggested to arise from high thermal stability of the enzyme coupled with X-ray-induced reduction of T1Cu, resulting in electron transfer (ET) to T2Cu.…”

Section: Introductionmentioning

confidence: 99%

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An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase

Halsted

Yamashita

Hirata

et al. 2018

Int Union Crystallogr J

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Synchrotron-based X-ray structural studies of ligand-bound enzymes are powerful tools to further our understanding of reaction mechanisms. For redox enzymes, it is necessary to study both the oxidized and reduced active sites to fully elucidate the reaction, an objective that is complicated by potential X-ray photoreduction. In the presence of the substrate, this can be exploited to construct a structural movie of the events associated with catalysis. Using the newly developed approach of serial femtosecond rotation crystallography (SF-ROX), an X-ray damage-free structure of the as-isolated copper nitrite reductase (CuNiR) was visualized. The sub-10 fs X-ray pulse length from the SACLA X-ray free-electron laser allowed diffraction data to be collected to 1.6 Å resolution in a 'time-frozen' state. The extremely short duration of the X-ray pulses ensures the capture of data prior to the onset of radiation-induced changes, including radiolysis. Unexpectedly, an O 2 ligand was identified bound to the T2Cu in a brand-new binding mode for a diatomic ligand in CuNiRs. The observation of O 2 in a time-frozen structure of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O 2 binding in CuNiRs. This provides an insight into how CuNiR from Alcaligenes xylosoxidans can function as an oxidase, reducing O 2 to H 2 O 2 , or as a superoxide dismutase (SOD) since it was shown to have $56% of the dismutase activity of the bovine SOD enzyme some two decades ago.

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Section: Comparison Of Srx Rs and Sf-rox Structuressupporting

confidence: 66%

Section: Comparison Of Srx Rs and Sf-rox Structuresmentioning

confidence: 63%

Section: Introductionmentioning

confidence: 99%

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An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase

Halsted

Yamashita

Hirata

et al. 2018

Int Union Crystallogr J

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“…(A) The nitrite-complex (PDB code 3WKP), 52 note the monodentate binding of nitrite via a single O atom, the substitution of Ile CAT with a Val residue and the steric restriction of the gatekeeper Asp CAT (Asp98) conformation (seen in other CuNiRs) by Phe110, resulting in only the proximal conformation being observed; (B) oxygen binding to GtNiR (PDB code 3WNJ). 61 Note that partially occupied water molecules are omitted for clarity. Cu atoms are shown as cyan spheres.…”

Section: Substrate and Copper Access To The T2cu Sitementioning

confidence: 99%

Recent structural insights into the function of copper nitrite reductases

et al. 2017

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Copper nitrite reductases (CuNiR) carry out the first committed step of the denitrification pathway of the global nitrogen cycle, the reduction of nitrite (NO) to nitric oxide (NO). As such, they are of major agronomic and environmental importance. CuNiRs occur primarily in denitrifying soil bacteria which carry out the overall reduction of nitrate to dinitrogen. In this article, we review the insights gained into copper nitrite reductase (CuNiR) function from three dimensional structures. We particularly focus on developments over the last decade, including insights from serial femtosecond crystallography using X-ray free electron lasers (XFELs) and from the recently discovered 3-domain CuNiRs.

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“…This was unexpected, as no nitrite or nitrogen source was added to the crystallization conditions (1.6 M sodium citrate and 50 mM Tris at a pH of 7.8). However, previous structural studies of bacterial copper nitrite reductases have revealed endogenous ligands bound to the T-2 site (Antonyuk et al, 2005;Fukuda et al, 2015). Both NO 2 À and NO have been shown to be bound in the Achromobacter cycloclastes T-2 copper site without being added to the crystal (Fig.…”

Section: Resultsmentioning

confidence: 93%

Structure and mechanism of copper–carbonic anhydrase II: a nitrite reductase

Andring

Kim

McKenna

2020

Int Union Crystallogr J

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Nitric oxide (NO) promotes vasodilation through the activation of guanylate cyclase, resulting in the relaxation of the smooth muscle vasculature and a subsequent decrease in blood pressure. Therefore, its regulation is of interest for the treatment and prevention of heart disease. An example is pulmonary hypertension which is treated by targeting this NO/vasodilation pathway. In bacteria, plants and fungi, nitrite (NO2 −) is utilized as a source of NO through enzymes known as nitrite reductases. These enzymes reduce NO2 − to NO through a catalytic metal ion, often copper. Recently, several studies have shown nitrite reductase activity of mammalian carbonic anhydrase II (CAII), yet the molecular basis for this activity is unknown. Here we report the crystal structure of copper-bound human CAII (Cu–CAII) in complex with NO2 − at 1.2 Å resolution. The structure exhibits Type 1 (T-1) and 2 (T-2) copper centers, analogous to bacterial nitrite reductases, both required for catalysis. The copper-substituted CAII active site is penta-coordinated with a `side-on' bound NO2 −, resembling a T-2 center. At the N terminus, several residues that are normally disordered form a porphyrin ring-like configuration surrounding a second copper, acting as a T-1 center. A structural comparison with both apo- (without metal) and zinc-bound CAII (Zn–CAII) provides a mechanistic picture of how, in the presence of copper, CAII, with minimal conformational changes, can function as a nitrite reductase.

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Insights into unknown foreign ligand in copper nitrite reductase

Cited by 8 publications

References 36 publications

An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase

An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase

Recent structural insights into the function of copper nitrite reductases

Structure and mechanism of copper–carbonic anhydrase II: a nitrite reductase

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