Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens

Tikhonova, Т. V.; Slutskaya, E. S.; Filimonenkov, A. A.; Boyko, K.М.; Kleimenov, S. Yu.; Konarev, Petr V.; Polyakov, K. M.; Svergun, Dmitri I.; Trofimov, A.A.; Khomenkov, V. G.; Zvyagilskaya, R. A.; Popov, Vladimir O.

doi:10.1134/s0006297908020077

Cited by 8 publications

(5 citation statements)

References 36 publications

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“…TvPaR and TvNiR were purified with a two‐step chromatography procedure described earlier in detail for TvNiR . The procedure involves ion exchange chromatography on DEAE‐Sepharose and size‐exclusion chromatography on Superdex 200.…”

Section: Methodsmentioning

confidence: 99%

“…A comparative sequence analysis of multiheme cytochromes c from GenBank revealed a family of putative octaheme nitrite reductases with a common signature motif, CXXCK . The first representative of this family, from the nitrate‐reducing obligately chemolithoautotrophic haloalkaliphilic sulfur‐oxidizing bacterium Thioalkalivibrio nitratireducens strain ALEN 2 (TvNiR) , has been purified and characterized .…”

Section: Introductionmentioning

confidence: 99%

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Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species

et al. 2012

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Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivibrio species was performed. It was shown that both enzymes have similar catalytic properties, owing to high structural similarity. Both enzymes are characterized by specific structural features distinguishing them from pentaheme cytochrome c nitrite reductases, such as the Tyr-Cys bond in the active site, the hexameric structure resulting in the formation of a void space inside the hexamer, and the product channel that opens into the void interior space of the hexamer. It is suggested that these specific structural features are responsible for the higher nitrite reductase activity, the greater preference for nitrite than for sulfite as a substrate, and the wider pH range of the catalytic activity of octaheme nitrite reductases than of pentaheme homologs.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species

et al. 2012

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“…The octa-haem CcNiR (Thialkalivibrio nitratireducens − and Thioalkalivibrio paradoxus ) is a homohexameric enzyme containing eight haems per monomer. The monomer of the octa-haem CcNiR consists of two domains: one N-terminal domain, with three haems in a unique fold, and one catalytic C-terminal domain, with five haems in an arrangement similar to that found in the penta-haem CcNiR.…”

Section: Biological Mechanistic Strategies To Handle Nitritementioning

confidence: 99%

How Biology Handles Nitrite

2014

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Introduction 5273 2. Biological Fate of Nitrite 5274 2.1. Biological Fate of Nitrite − Nitrite in the Nitrogen Cycle 5274 2.1.1. Classic and New Pathways 5274 2.1.2. Nitrite and Nitrogen "Recycling" 5277 2.2. Biological Fate of Nitrite − Nitrite in Signaling Pathways 5277 2.2.1. Nitrite in Signaling Pathways in Mammals 5277 2.2.2. Nitrite in Signaling (and Other) Pathways in Plants 5297 2.2.3. Nitrite in Signaling (and Other) Pathways in Bacteria 5303 3. Biological Mechanistic Strategies To Handle Nitrite 5305 3.1. Nitrite Reduction to Ammonium 5306 3.1.1.

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“…This accounts for the extremely high resistance of the enzyme to dissociation. 18 The dissociation of the TvNiR hexamer in solution was observed only in the presence of urea and guanidine chloride at high concentrations. In accordance with the relative contributions of the dimeric and trimeric contacts to the formation of the native structure, 17,18 the dissociation proceeds at the dimeric contact to form trimers followed by dissociation of the latter into monomers; no formation of dimers was observed during dissociation of TvNiR.…”

Section: Quaternary Structurementioning

confidence: 99%

“…17 Like NrfAs, TvNiR catalyzes the reduction of nitrite and hydroxylamine to ammonia without release of any intermediates. In solution, TvNiR exists as a stable hexamer containing 48 hemes c. 17,18 Despite only ∼ 20% sequence identity with the structurally characterized NrfAs, the catalytically important active-site residues, as well as four CXXCH motifs and one CXXCK hemebinding motif of the NrfA sequences, are conserved in the TvNiR sequence. TvNiR shows no sequence similarity with HAO or OTR.…”

Section: Introductionmentioning

confidence: 99%

High-Resolution Structural Analysis of a Novel Octaheme Cytochrome c Nitrite Reductase from the Haloalkaliphilic Bacterium Thioalkalivibrio nitratireducens

Polyakov

Boyko

Tikhonova

et al. 2009

Journal of Molecular Biology

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Bacterial pentaheme cytochrome c nitrite reductases (NrfAs) are key enzymes involved in the terminal step of dissimilatory nitrite reduction of the nitrogen cycle. Their structure and functions are well studied. Recently, a novel octaheme cytochrome c nitrite reductase (TvNiR) has been isolated from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Here we present high-resolution crystal structures of the apoenzyme and its complexes with the substrate (nitrite) and the inhibitor (azide). Both in the crystalline state and in solution, TvNiR exists as a stable hexamer containing 48 hemes-the largest number of hemes accommodated within one protein molecule known to date. The subunit of TvNiR consists of two domains. The N-terminal domain has a unique fold and contains three hemes. The catalytic C-terminal domain hosts the remaining five hemes, their arrangement, including the catalytic heme, being identical to that found in NrfAs. The complete set of eight hemes forms a spatial pattern characteristic of other multiheme proteins, including structurally characterized octaheme cytochromes. The catalytic machinery of TvNiR resembles that of NrfAs. It comprises the lysine residue at the proximal position of the catalytic heme, the catalytic triad of tyrosine, histidine, and arginine at the distal side, channels for the substrate and product transport with a characteristic gradient of electrostatic potential, and, finally, two conserved Ca(2+)-binding sites. However, TvNiR has a number of special structural features, including a covalent bond between the catalytic tyrosine and the adjacent cysteine and the unusual topography of the product channels that open into the void interior space of the protein hexamer. The role of these characteristic structural features in the catalysis by this enzyme is discussed.

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Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens

Cited by 8 publications

References 36 publications

Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species

Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species

How Biology Handles Nitrite

High-Resolution Structural Analysis of a Novel Octaheme Cytochrome c Nitrite Reductase from the Haloalkaliphilic Bacterium Thioalkalivibrio nitratireducens

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