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1.7.2.2: nitrite reductase (cytochrome; ammonia-forming)

This is an abbreviated version!
For detailed information about nitrite reductase (cytochrome; ammonia-forming), go to the full flat file.

Word Map on EC 1.7.2.2

Reaction

NH3
+ 2 H2O + 6 ferricytochrome c =
nitrite
 + 6 ferrocytochrome c + 7 H+

Synonyms

ammonia-forming cytochrome c nitrite reductase, ccNiR, CcuHao, CfHao, CmHao, cNiR, cytochrome c NiR, cytochrome c nitrite reductase, cytochrome c nitrite reductase complex, cytochrome c-552, epsilonHao, epsilonproteobacterial hydroxylamine oxidoreductase, Glov_1042, haoA, hexaheme c-type cytochrome, More, multihaem c NiR, multiheme cytochrome c nitrite reductase, multiheme nitrite reductase, NiR, NiR cytochrome c552, nirB, NirC, nitrite reductase, NpHao, NrfA, NrfA2NrfH complex, NrfHA, octahaem cytochrome c nitrite reductase, SCO2486, SCO2488, TvNiR, WS0969

ECTree

     1 Oxidoreductases
         1.7 Acting on other nitrogenous compounds as donors
             1.7.2 With a cytochrome as acceptor
                1.7.2.2 nitrite reductase (cytochrome; ammonia-forming)

Crystallization

Crystallization on EC 1.7.2.2 - nitrite reductase (cytochrome; ammonia-forming)

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method, structure determined to 2.3 A resolution
-
crystals are grown by the vapour-diffusion technique by mixing equal amounts of protein and reservoir solution, which contains about 10% (w/v) PEG 4K in 0.1 M HEPES pH 7.5 buffer
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mutant H264N, to 2.15 A resolution. Homodimeric protein, the constellation of His/His and Lys-coordinated c-hemes is indistinguishable from those of the native enzyme
purified NrfA, hanging drop vapor diffusion method, five conditions that result in several different crystal packing motifs, e.g. 0.001 ml of protein solution containing 10 mg/ml of NrfA mixed with 0.001 ml of mother liquor containing 100 mM HEPES, pH 7.5, 20% PEG 10000 and incubated in hanging drop trays with a 1 ml well solution at 4°C, 5-14 days, other conditions, overview. X-ray diffraction structure determination and analysis at 1.7-2.5 A resolution
purified recombinant wild-type and mutant Q263E, 10 mg/ml protein, under aerobic conditions by the vapor diffusion hanging drop method using 20% v/v PEG 10000 in 100 mM Na-HEPES, pH 7.5, 20% ethylene glycol as cryoprotectant, X-ray diffraction structure determination and analysis at 1.74 A and 2.04 A resolution, respectively, molecular replacement
vapour diffusion method. Crystals belong to space group P2(1)2(1)2(1) with apparent cell parameters of a = 81.47 A, b = 90.84 and c = 294.87 A and contain four molecules of NrfA per asymmetric unit
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crystallization of cytochrome c552, 2.2 A resolution
Marinobacter nauticus
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UV/Vis spectropotentiometric results yield highly reproducible values for the heme midpoint potentials, which can be assigned to specific hemes in each protomer. Addition of the strong-field ligand cyanide leads to a 70 mV positive shift of the active site's midpoint potential, the cyanide binds to the initially 5-coordinate high-spin heme and triggers a high-spin to low-spin transition. With cyanide present three of the remaining hemes give rise to distinctive and readily assignable EPR spectral changes upon reduction
alone or in complex with nitrite and cyanide, hanging drop vapor diffusion method, using 0.2 M trisodium citrate dihydrate, 0.1 M Tris-HCl pH 8.5 and 30% (v/v) PEG 400
Q5F2I3
apoenzyme and its complexes with the substrate nitrite and the inhibitor azide. The subunit of NiR consists of the N-terminal domain which has an unique fold and contains three hemes and the catalytic C-terminal domain which hosts the remaining five hemes. The complete set of eight hemes forms a spatial pattern characteristic of other multiheme proteins, including structurally characterized octaheme cytochromes. The catalytic machinery 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, two conserved Ca2+-binding sites. In addition, the enzyme has a covalent bond between the catalytic tyrosine and the adjacent cysteine and an unusual topography of the product channels that open into the void interior space of the protein hexamer
Q5F2I3
diffraction data sets with increasing absorbed doses. The structures reveal gradual changes associated with the reduction of the catalytic hemes by X-rays. The conversion of the nitrite ions bound in the active sites to NO species is observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic heme and the iron ion of the heme takes place. In the sulfite complex no enzymatic reaction is detected
hanging drop vapour diffusion method
-
modified form of the enzyme that contains an additional covalent bond between residues Tyr303 and Gln360 in complex with phosphate to 1.45 A resolution, and with sulfite to 1.8 A resolution, structure of unmodified enzyme in complex with nitrite to 1.83 A resolution. Structure reveal the presence of a covalent bond between the CE2 atom of the catalytic Tyr303 and the S atom of Cys305, which might be responsible for the higher nitrite reductase activity. The formation of the second covalent bond by Tyr303 leads to a decrease in both the nitrite and sulfite reductase activities of the enzyme. Tyr303 is located at the exit from the putative proton-transport channel to the active site
Q5F2I3
structure at 2.55 A resolution, presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes
Trichlorobacter lovleyi
ccNIR as apoenzyme or with bound sulfite or nitrite to the catalytic heme center, X-ray diffraction structure determination and analysis at 1.30-1.75 A resolution
enzyme in complex with nitrite
-
sitting drop vapour diffusion using ammonium sulfate as precipitant. Crystal growth of the NrfHA complex is strongly dependent on the presence of detergent, presumably because of the need to shield the hydrophobic transmembrane helix of NrfH from the solvent. The crystals grown belong to space group I422
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Triton X-114 significant improvement in crystal size and quality
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