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Literature summary extracted from

  • Lintuluoto, M.; Lintuluoto, J.M.
    DFT study on enzyme turnover including proton and electron transfers of copper-containing nitrite reductase (2016), Biochemistry, 55, 4697-4707 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.7.2.1 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 Geobacillus thermodenitrificans

Protein Variants

EC Number Protein Variants Comment Organism
1.7.2.1 C135A mutant structure analysis, nitrite bound to the T2 Cu site in the eta1-O end-on form, structure analysis, PDB ID 3WKP 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
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
1.7.2.1 nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+ the proposed mechanisms for the reduction of nitrite by CuNiRs include intramolecular electron and proton transfers, proton-coupled electron transfer is one of the key processes in enzyme reactions, density functional theory calculations analysis. The reduction of T2 Cu site promotes the proton transfer, and the hydrogen bond network around the binding site has an important role not only to stabilize the nitrite binding but also to promote the proton transfer to nitrite. Reaction mechanism, overview 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
-
 ?

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 additional information geometric structure of the nitrite-bound T2 Cu site in GtNiR using density functional theory, DFT, calculations. The reduction of T2 Cu site promotes the proton transfer. Optimized structures of nitrite binding forms under physiological pH conditions and in neutral states, detailed overview Geobacillus thermodenitrificans
1.7.2.1 physiological function dissimilatory reduction of nitrite by copper-containing nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle Geobacillus thermodenitrificans