Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Fukuda, Y.; Tse, K.M.; Lintuluoto, M.; Fukunishi, Y.; Mizohata, E.; Matsumura, H.; Takami, H.; Nojiri, M.; Inoue, T.
    Structural insights into the function of a thermostable copper-containing nitrite reductase (2014), J. Biochem., 155, 123-135 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.7.2.1 gene nirK, recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Geobacillus thermodenitrificans

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.7.2.1 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 Geobacillus thermodenitrificans

Protein Variants

EC Number Protein Variants Comment Organism
1.7.2.1 C135A site-directed mutagenesis, the crystal structure of mutant C135A with nitrite displays a unique eta1-O coordination mode of nitrite at the catalytic copper site (T2Cu) unlike the wild-type enzyme Geobacillus thermodenitrificans

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.7.2.1 periplasm
-
 Geobacillus thermodenitrificans
-
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.7.2.1 Cu2+ homotrimeric CuNIR contains one type 1 (T1Cu) and one type 2 Cu (T2Cu) site per monomer. The T1Cu atom is coordinated by four amino acid residues (two histidine residues, cysteine and methionine) and functions as a receptor site for the electron supplied by an electron-donor protein such as c-type heme-containing cytochrome or blue-copper proteins. The T2Cu site is a catalytic centre composed of three histidine residues and an axial ligand water molecule. Copper centre structure, overview Geobacillus thermodenitrificans

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.7.2.1 nitrite + ferrocytochrome c + 2 H+ Geobacillus thermodenitrificans
-
 nitric oxide + H2O + ferricytochrome c
-
 ?
1.7.2.1 nitrite + ferrocytochrome c + 2 H+ Geobacillus thermodenitrificans NG80-2
-
 nitric oxide + H2O + ferricytochrome c
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.7.2.1 Geobacillus thermodenitrificans A4IL26
-
-
1.7.2.1 Geobacillus thermodenitrificans NG80-2 A4IL26
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.7.2.1 recombinant wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by ammonium sulfate fractionation, hydrophobic interaction chromatography, dialysis, and anion exchange chromatography, followed by gel filtration Geobacillus thermodenitrificans

Reaction

EC Number Reaction Comment Organism Reaction ID
1.7.2.1 nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+ reaction mechanism, overview. 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 CH-O hydrogen bond observed between His244 and water, respectively. Analysis of the hydrogen-bond networks around His244 and the flow path of protons consumed by nitrite reduction. The electron transfer reaction is coupled with the proton transfer reaction Geobacillus thermodenitrificans
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.7.2.1 nitrite + ferrocytochrome c + 2 H+
-
 Geobacillus thermodenitrificans nitric oxide + H2O + ferricytochrome c
-
 ?
1.7.2.1 nitrite + ferrocytochrome c + 2 H+
-
 Geobacillus thermodenitrificans NG80-2 nitric oxide + H2O + ferricytochrome c
-
 ?

Subunits

EC Number Subunits Comment Organism
1.7.2.1 homotrimer 3 * 35478, sequence calculation Geobacillus thermodenitrificans
1.7.2.1 More CuNIR typically has a homotrimeric structure containing one type 1 (T1Cu) and one type 2 Cu (T2Cu) site per monomer Geobacillus thermodenitrificans

Synonyms

EC Number Synonyms Comment Organism
1.7.2.1 copper-containing nitrite reductase
-
 Geobacillus thermodenitrificans
1.7.2.1 CuNIR
-
 Geobacillus thermodenitrificans
1.7.2.1 GtNiR
-
 Geobacillus thermodenitrificans
1.7.2.1 NirK
-
 Geobacillus thermodenitrificans

Cofactor

EC Number Cofactor Comment Organism Structure
1.7.2.1 cytochrome c
-
 Geobacillus thermodenitrificans

General Information

EC Number General Information Comment Organism
1.7.2.1 metabolism the enzyme catalyzes the key reaction in denitrification as the nitrogen compound is changed from an ionic state to a gaseous molecule Geobacillus thermodenitrificans
1.7.2.1 physiological function copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO2 ) to nitric oxide (NO) during denitrification Geobacillus thermodenitrificans