Crystallization (Comment) | Organism |
---|---|
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 | Comment | Organism |
---|---|---|
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 | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
nitrite + ferrocytochrome c + 2 H+ | Geobacillus thermodenitrificans | - |
nitric oxide + H2O + ferricytochrome c | - |
? | |
nitrite + ferrocytochrome c + 2 H+ | Geobacillus thermodenitrificans NG80-2 | - |
nitric oxide + H2O + ferricytochrome c | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Geobacillus thermodenitrificans | A4IL26 | - |
- |
Geobacillus thermodenitrificans NG80-2 | A4IL26 | - |
- |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
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 |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
nitrite + ferrocytochrome c + 2 H+ | - |
Geobacillus thermodenitrificans | nitric oxide + H2O + ferricytochrome c | - |
? | |
nitrite + ferrocytochrome c + 2 H+ | - |
Geobacillus thermodenitrificans NG80-2 | nitric oxide + H2O + ferricytochrome c | - |
? |
Synonyms | Comment | Organism |
---|---|---|
copper-containing nitrite reductase | - |
Geobacillus thermodenitrificans |
CuNIR | - |
Geobacillus thermodenitrificans |
GtNiR | - |
Geobacillus thermodenitrificans |
NirK | - |
Geobacillus thermodenitrificans |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
cytochrome c | - |
Geobacillus thermodenitrificans |
General Information | Comment | Organism |
---|---|---|
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 |
physiological function | dissimilatory reduction of nitrite by copper-containing nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle | Geobacillus thermodenitrificans |