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1.7.2.1: nitrite reductase (NO-forming)

This is an abbreviated version!
For detailed information about nitrite reductase (NO-forming), go to the full flat file.

Word Map on EC 1.7.2.1

Reaction

nitric oxide
+
H2O
 +
ferricytochrome c
=
nitrite
 +
ferrocytochrome c
 + 2 H+

Synonyms

AcNIR, AfNiR, AniA, AxNiR, BRAO375_2740002, C551-O2 oxidoreductase, cd1 nitrite reductase, cd1NiR, cNOR, copper-containing dissimilatory nitrite reductase, copper-containing nitrite reductase, Cu-NIR, Cu-NirK, CuNIR, cytochrome c-551:O2, NO2- oxidoreductase, cytochrome cd, cytochrome cd1 nitrite reductase, cytochrome oxidase, dissimilatory nitrite reductase, dissimilatory nitrite reductase cytochrome cd1, EC 1.6.6.5, EC 1.7.99.3, EC 1.9.3.2, GK0767, GtNiR, HdNIR, hemoglobin, HydNIR, HYPDE_25578, KSU1_D0929, mARC1, mARC2, mitochondrial amidoxime reducing component, MRA2164, NiR, NiR-Pa, NirK, NirS, nitrite reductase, oxidase, Pseudomonas cytochrome, PaNiR, PNR, Pseudomonas cytochrome oxidase, PsNiR, reductase, nitrite (cytochrome), Rpic_4015, S58_68210

ECTree

     1 Oxidoreductases
         1.7 Acting on other nitrogenous compounds as donors
             1.7.2 With a cytochrome as acceptor
                1.7.2.1 nitrite reductase (NO-forming)

Crystallization

Crystallization on EC 1.7.2.1 - nitrite reductase (NO-forming)

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
atomic resolution structures of four forms of the green Cu-nitrite reductase: structure of the resting state of the enzyme at 0.9 A, structure of then nitrite-soaked complex at 1.10 A resolution, structure of the endogenously bound NO complex at 1.12-A resolution, structure of endogenously bound nitrite and NO in the same crystal at 1.15-A resolution
mutant H254F loaded with either Cu2+ or Zn2+, to 1.5 A and 1.85 A, respectively. Both structures are essentially identical. Structure of mutant N90S, to 1.6 A resolution. In both the native and mutant N90S structures, a surface Zn ion is present in each monomer, bridging the two monomers through the coordinating residues His165 and Asp167 of one monomer and Glu195 of the adjacent monomer. This Zn site is similar to that described previously in several NiR structures
sitting-drop vapour diffusion method. Crystal structures of M144L and M144Q at 1.9 A, crystal structure of native enzyme at 1.04 A, structure of mutant enzyme C130A at 1.35 A
-
use of crystallography, together with online X-ray absorption spectroscopy and optical spectroscopy, to show that X-rays rapidly and selectively photoreduce the type 1 Cu centre, but that the type 2 Cu centre does not photoreduce directly over a typical crystallographic data collection time. Internal electron transfer between the type 1 Cu and type 2 Cu centres does not occur, and the type 2 Cu centre remains oxidized
crystals are grown at 19°C by hanging drop vapour diffusion using a reservoir of 100 mM sodium acetate, pH 4.7, 6%-10% polyethylene glycol 4000 and 1-5 mM cupric chloride, each drop is made from an equal volume of reservoir and a 15 mg/ml protein stock solution buffered in 10 mM Tris pH 7.0, crystals of mutants diffract to 1.8 A, nitrite-soaked oxidized crystals are obtained by placing crystals in reservoir solution supplemented with 5 mM sodium nitrite
-
hanging-drop vapor-diffusion method, mutant enzyme M150G
M150G crystals are grown at room temperature by hanging drop vapor diffusion method
-
purified recombinant enzyme, free or in complex with small molecule inhibitors, hanging drop vapor diffusion method, room temperature, 25 mg/ml protein in 20 mM Tris-HCl, pH 7.0, is mixed with an equal volume of reservoir containing 6-10% PEG 4000, 100 mM sodium acetate, pH 4.0, addition of 20 mM of ligands 20 mM of azide, formate, or nitrate, X-ray diffraction structure determination and analysis at 1.5-1.8 A resolution
recombinant soluble domain, residues 483-913, to 2.4 A
structures of copper-containing nitrite reductase NiR and the N-terminal 68 residue-deleted mutant, at resolutions of 1.3 A and 1.8 A, respectively. Both structures show a striking resemblance with the overall structure of the well-known copper-containing nitrite reductases composed of two Greek key beta-barrel domains. The N-terminal region has one beta-strand and one alpha-helix extended to the northern surface of the type-1 copper site. This region contributes to the transient binding with the partner protein during the interprotein electron transfer reaction in the Geobacillus system. The region is directly involved in the specific partner recognition
crystal structure analysis and computational modelling, the model includes the T2 Cu site, the nitrite, three His residues coordinated to the T2 Cu site, and the second sphere residues Asp98, His244, and Val246. Additionally, two water molecules are included. One water molecule is labeled WAT1 occupying an intermediate position between Asp98 and His244 and another is labeled WAT2 and seems to interact with Asp98 in the initial coordinates of the X-ray structure, from PDB ID 3WKP
purified wild-type enzyme with chloride- and formate-bound, as well as purified enzyme mutant C135A with nitrite-bound, hanging drop vapour diffusion method, mixng of 0.0015 ml of 100 mg/ml protein solution with 0.001 5 ml of well solution containing 0.1 M acetate buffer, pH 4.5, 5.0% w/v PEG 4000, 75 mM CuSO4, and 200 mM sodium formate, and equilibration against 0.45 ml well solution, soaking of C135A mutant crystals in nitrite solution, at 20°C, X-ray diffraction structure determination and analysis at 1.15 A and 1.90 A resolution, respectively
the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper site of NirK during anaerobic synchrotron-radiation crystallography experiments. The structure shows a dual conformation of one water molecule as an axial ligand in the type 2 copper site. In the structure of the C135A mutant with peroxide bound to the type 2 copper atom, the peroxide molecule is mainly observed in a side-on binding manner, with a possible minor end-on conformation
hanging drop vapour diffusion, 0.002 ml protein solution containing 20 mg/ml protein in 20 mM Tris-Hcl, pH 7.5 are mixed with reservoir solution containing 18% polyethylene glycol 4000 and 100 mM Tris-HCl, pH 8.9 at 20°C, crystals of wild-type HdNIR and C260A mutant diffract to 2.35 A and 3.5 A, respectively
-
in complex with its electron-donor protein pseudoazurin
-
the type 1 copper in the N-terminal tethered cupredoxin domain is placed too far away from the catalytic core type i copper for effective electron transfer. The N-terminal peptide that carries His27 plays a role in water-mediated anchoring of the substrate at the type 2 copper site
molecular docking simulations with cytochrome c552 or cytochrome c show that hydrophobic interactions favor the formation of complexes where the heme c domain of the enzyme is the principal docking site. Only for cytochrome c552 the preferential areas of contact and Fe-Fe distances between heme groups of the redox partners allow establishing competent electron transfer pathways. The coupling of the enzyme with chemical redox mediators is not energetically favorable
Marinobacter nauticus
-
crystal structure
-
crystals of Y25S mutant protein are grown from a solution containing 10-20 mg/ml protein in the presence of 2.2-2.4 M ammonium sulfate and 50 mM potassium phosphate, pH 7.0, crystals diffract to 1.4 A
-
molecular modeling of myglobin mutant L29H/F43Y with or without nitrite shows the necessary structural features of native cytochrome cd1 nitrite reductase and that the protein can provide comparable interactions with nitrite as in native nitrite reductase
-
to 1.95 A resolution. The naturally fused type of Cu-nitrite reductase tethering a cytochrome c at the C-terminus folds as a unique trimeric domain-swapped structure and has a self-sufficient electron flow system. The C-terminal cytochrome c domain is located at the surface of the type 1 copper site in the N-terminal domain from the adjacent subunit. The heme-to-Cu distance of 10.6 A is comparable to the transient electron transfer complex of normal Cu-nitrite reductase with cytochrome c. The cytochrome c-Cu-nitrite reductase domain interaction is highly transient. An electron is directly transferred from the partner to the type 1 copper
-
2.5 A resolution
-
crystals of the H327A mutant are obtained by vapor diffusion technique by mixing in a 1:1 ratio the protein and a reservoir solution containing 4.0% polyethylene glycol 5000 monomethyl ether, 0.1 M sodium acetate, pH 5.5. The space group is 4(3)22 with cell dimensions 70.5 x 70.5 x 281 A. Crystals of the H369A mutant are obtained by mixing in a 1.1 ratio the protein and a reservoir solution containing 11.5% polyethylene glycol 6000, 0.2 M imidazole/malate, pH 6.5. The space group is P4(1)2(1)2 with cell dimensions 94.7 x 94.7 x 159.9 A
crystals of the H327A mutants are obtained by vapour diffusion technique. Crystals of H369A are obtained by mixing equal volumes of a reservoir solution containing 11.5% PEG 6000, 0.2 M imidazole/malate, pH 6.5, and of protein, in presence or not of 50 mM potassium nitrite and 50 mM sodium ascorbate. Crystals belong to space group P4(1)2(1)2 with cell dimensions a = b = 94.7 A, c = 159.9 A. The three-dimensional structures of NIR mutant H327A, and H369A in complex with NO solved by multiple wave-length anomalous dispersion, using the iron anomalous signal, and molecular replacement techniques. In both refined crystal structures the c-heme domain, whilst preserving its classical c-type cytochrome fold, has undergone a 60° rigid-body rotation around an axis parallel with the pseudo 8-fold axis of the beta-propeller, and passing through residue Gln115. Even though the distance between the Fe ions of the c and d1-heme remains 21 A, the edge-to-edge distance between the two hemes has increased by 5 A. Furthermore the distal side of the d1-heme pocket appears to have undergone structural re-arrangement and Tyr10 has moved out of the active site. In the H369A-NO complex, the position and orientation of NO is significantly different from that of the NO bound to the reduced wild-type structure
-
H327A mutant enzymes: vapour diffusion technique, mixing of the enzyme and a reservoir solution containing 4% polyethylene glycol 5000 monomethyl ether, 100 mM sodium acetate pH 5.5 in a 1/1 ratio, H369A mutant enzyme: 11.5% polyethylene glycol 6000, 200 mM imidazole/malate pH 6.5, x-ray structure of both mutants
structure of the reduced enzyme both in the unbound form and with the physiological product, NO, bound at the d1 heme active site
the structure of the orthorhombic form (P2(1)2(1)2) of oxidized NiR-Pa is solved at 2.15 A resolution, using molecular replacement with the coordinates of the NiR from Thiosphaera pantotropha as the starting model
-
vapour diffusion at 20°C, in presence of 10% polyethylene glycol 4000, 50 mM Tris-HCl, pH 8.7, 400 mM NaCl, at a protein concentration of 14 mg/ml. The crystals are dark green elongated tetragonal prisms of dimensions 1.5 mm * 0.2 mm * 0.2 mm for the largest ones. These crystals are tetragonal with space group P4(1)(3)2(1)2 and cell dimensions a = b = 128.2 A, c = 172.6 A. They diffract at least up to 2.8 A
-
structures of copper(I)-nitrite complexes with sterically hindered tris(4-imidazolyl)carbinols such as tris(1-methyl-2-ethyl-4-imidazolyl)carbinol, tris(1-methyl-2-isopropyl-4-imidazolyl)carbinol, or tris(1-pyrazolyl)methanes such as tris(3,5-dimethyl-1-pyrazolyl)methane or tris(3,5-diethyl-1-pyrazolyl)methane, and tris(3,5-diisopropyl-1-pyrazolyl)methane reveal mononoclear ny1-N-bound nitrite complexes with a distorted tetrahedral geometry
-
homology modeling based on PDB entry 1BKW. Model demonstrates that the enzyme can be folded into two cupredoxin domains of the well-known CuNIR structure and implies that the conserved residues H122, D125, H127, H158, C159, H168, M173,H272, and H321 form the type 1 and type 2 Cu sites
-