Molecular Structure of Nitro- and Nitrito-Copper Complexes as Reaction Intermediates in Electrochemical Reduction of Nitrite to Dinitrogen Oxide

Komeda, Nobutoshi; Nagao, Hidemi; Kushi, Yoshihiko; Adachi, Gin‐ya; Suzuki, Masatatsu; Uehara, Akira; Tanaka, Koji

doi:10.1246/bcsj.68.581

Cited by 66 publications

(77 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…A monodentate coordination mode has never been observed in other wild-type T2Cu sites in CuNIR structures in which nitrite adopts an Z 2 O,O binding mode (17,18). The distance between the O2 atom (closest to the T2Cu atom) of nitrite and the T2Cu atom is 1.97 Å , which is slightly shorter than the distances observed in the Z (40,41). A refined average B-factor of 31 Å 2 indicates that the nitrite ion is well ordered.…”

Section: Structure Of a Thermostable Cunirmentioning

confidence: 76%

Structural insights into the function of a thermostable copper-containing nitrite reductase

Fukuda¹,

Tse²,

Lintuluoto³

et al. 2013

The Journal of Biochemistry

View full text Add to dashboard Cite

Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO À 2 ) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride-and formate-bound forms of wild type at 1.15 Å resolution and the nitrite-bound form of the C135A mutant at 1.90 Å resolution. The structure of C135A with nitrite displays a unique g 1 -O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wildtype CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CHO hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the g 1 -O coordination manner is proposed.

show abstract

Section: Structure Of a Thermostable Cunirmentioning

confidence: 76%

Structural insights into the function of a thermostable copper-containing nitrite reductase

Fukuda¹,

Tse²,

Lintuluoto³

et al. 2013

The Journal of Biochemistry

View full text Add to dashboard Cite

show abstract

“…Complex 4 exhibits an intense broad band around 320 nm (ε Ϸ 5000 m -1 cm -1 ), which is assigned to a Cu I Ǟ NO 2 -MLCT transition. [10][11][12][13][14] The cyclic voltammogram of 2 in H 2 O shows a response with E 1/2 = -95 mV vs. Ag/AgCl and a peak-to-peak sepa-ration, ΔE, of 74 mV in the presence of 500 mm NaNO 2 (a in Figure 5). The ΔE value indicates a quasi-reversible electron-transfer process.…”

Section: Introductionmentioning

confidence: 99%

“…Figure 1 shows the X-ray crystal structures of 1 and 2. [10][11][12][13][14] and the nitrite-binding type-2 Cu II site in nitrite-soaked NIR at 1.4 Å resolution (Cu-O = 2.29-2.38, 2.04-2.08 Å). [9] The Cu, N(4) , some important structural aspects are different.…”

Section: Introductionmentioning

confidence: 99%

Cu^I and Cu^II Complexes Containing Nitrite and Tridentate Aromatic Amine Ligand as Models for the Substrate‐Binding Type‐2 Cu Site of Nitrite Reductase

et al. 2005

View full text Add to dashboard Cite

CuI and CuII complexes containing a tridentate aromatic amine compound [bis(6‐methyl‐2‐pyridylmethyl)amine, Me2bpa] in the absence and presence of nitrite have been prepared as models for the active site of dissimilatory copper‐containing nitrite reductase (CuNIR). [CuII(Me2bpa)(H2O)(ClO4)]ClO4 (1), [CuII(Me2bpa)(NO2)(ClO4)] (2), [CuI(Me2‐bpa)(CH3CN)]PF6 (3) and [CuI(Me2bpa)(NO2)]2·[(Ph3P)2‐NPF6] (4) were prepared. The X‐ray crystal structural analyses of 1, 2, and 4 reveal that the geometries of the Cu centers are distorted square pyramidal, distorted octahedral, and tetrahedral, respectively. The coordination modes of the nitrite ligands in 2 and 4 depend on the oxidation state of the copper ion: nitrite is coordinated to CuII and CuI through two oxygen atoms (O,O'‐coordination mode) and one nitrogen atom (N‐coordination mode), respectively. A comparison of the absorption spectra of 1 and 2 in acetone solution indicates that the 387‐nm absorption band (ϵ = 780 M–1 cm–1) of 2 is a charge‐transfer transition. The broad absorption band at around 320 nm (ϵ ≈ 5000 M–1 cm–1) of 4 in dichloromethane is also due to a charge‐transfer transition. Functional modeling of CuNIR has been accomplished by treating solutions of 4 with acid; the nitrite‐binding CuI complex quantitatively gives the one‐electron reduction product,NO. The nitrite reduction of 4 in dichloromethane obeys a second‐order rate law, suggesting that the rate‐determining step would be protonation of the nitrite ligand of 4. Electronic structure calculations of the CuI and CuII complexes containing Me2bpa and nitrite by the density functional theory method demonstrate that the net charge of nitrite in CuI(Me2bpa)(nitro) is larger than that in CuI(Me2bpa)(nitrito). The mechanism of the nitrite reduction is discussed in comparison with the enzyme reaction mechanism of CuNIR. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

show abstract

“…It is clear from the pH profile that higher activities can be achieved at even lower pH, although these rates are still not competitive with NiR. Numerous other mononuclear models that examine NiR reactivity have been explored so far (31,36,(47)(48)(49)(50). These compounds are split into those whose activities have been investigated in nonaqueous solutions (34,49,50) and those that have been examined in aqueous solutions (47,48,(51)(52)(53)(54).…”

mentioning

confidence: 99%

“…There are only a few examples of functional copper complexes that can reduce nitrite in aqueous solutions, and in general these systems have far lower rates that those observed in nonaqueous conditions. In some cases, these complexes produced N 2 O rather than NO (48, 54), whereas the systems in which multiple turnovers were observed have been associated mostly with electrocatalytic reactions, particularly heterogeneous systems (i.e., catalyst linked to the electrode surface) (47,48,51,54). One example has been reported of a copper complex capable of at least four turnovers in 15 min when reduced using photoactivated [Ru(II)(bpy) 3 ] 2+ as the electron donor, but with a significant decrease in activity (NO generation) after two turnovers (52).…”

mentioning

confidence: 99%

Designing a functional type 2 copper center that has nitrite reductase activity within α-helical coiled coils

Tegoni

Yu²,

Bersellini

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

101

188

View full text Add to dashboard Cite

One of the ultimate objectives of de novo protein design is to realize systems capable of catalyzing redox reactions on substrates. This goal is challenging as redox-active proteins require design considerations for both the reduced and oxidized states of the protein. In this paper, we describe the spectroscopic characterization and catalytic activity of a de novo designed metallopeptide Cu(I/II)(TRIL23H) 3 +/2+ , where Cu(I/II) is embeded in α-helical coiled coils, as a model for the Cu T2 center of copper nitrite reductase. In Cu(I/II)(TRIL23H) 3 +/2+ , Cu(I) is coordinated to three histidines, as indicated by X-ray absorption data, and Cu(II) to three histidines and one or two water molecules. Both ions are bound in the interior of the three-stranded coiled coils with affinities that range from nano- to micromolar [Cu(II)], and picomolar [Cu(I)]. The Cu(His) 3 active site is characterized in both oxidation states, revealing similarities to the Cu T2 site in the natural enzyme. The species Cu(II)(TRIL23H) 3 2+ in aqueous solution can be reduced to Cu(I)(TRIL23H) 3 + using ascorbate, and reoxidized by nitrite with production of nitric oxide. At pH 5.8, with an excess of both the reductant (ascorbate) and the substrate (nitrite), the copper peptide Cu(II)(TRIL23H) 3 2+ acts as a catalyst for the reduction of nitrite with at least five turnovers and no loss of catalytic efficiency after 3.7 h. The catalytic activity, which is first order in the concentration of the peptide, also shows a pH dependence that is described and discussed.

show abstract

Molecular Structure of Nitro- and Nitrito-Copper Complexes as Reaction Intermediates in Electrochemical Reduction of Nitrite to Dinitrogen Oxide

Cited by 66 publications

References 50 publications

Structural insights into the function of a thermostable copper-containing nitrite reductase

Structural insights into the function of a thermostable copper-containing nitrite reductase

Cu^I and Cu^II Complexes Containing Nitrite and Tridentate Aromatic Amine Ligand as Models for the Substrate‐Binding Type‐2 Cu Site of Nitrite Reductase

Designing a functional type 2 copper center that has nitrite reductase activity within α-helical coiled coils

Contact Info

Product

Resources

About

Molecular Structure of Nitro- and Nitrito-Copper Complexes as Reaction Intermediates in Electrochemical Reduction of Nitrite to Dinitrogen Oxide

Cited by 66 publications

References 50 publications

Structural insights into the function of a thermostable copper-containing nitrite reductase

Structural insights into the function of a thermostable copper-containing nitrite reductase

CuI and CuII Complexes Containing Nitrite and Tridentate Aromatic Amine Ligand as Models for the Substrate‐Binding Type‐2 Cu Site of Nitrite Reductase

Designing a functional type 2 copper center that has nitrite reductase activity within α-helical coiled coils

Contact Info

Product

Resources

About

Cu^I and Cu^II Complexes Containing Nitrite and Tridentate Aromatic Amine Ligand as Models for the Substrate‐Binding Type‐2 Cu Site of Nitrite Reductase