Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Cu2+ | each monomer of the trimeric enzyme contains two copper sites: type I (T1) and type II (T2), which are connected via a cysteine (Cys)-histidine (His) bridge for rapid electron transfer. T1 and T2 copper sites structure, PDB ID 2BWD | Achromobacter cycloclastes |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
nitrite + ferrocytochrome c + 2 H+ | Achromobacter cycloclastes | - |
nitric oxide + H2O + ferricytochrome c | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Achromobacter cycloclastes | P25006 | - |
- |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+ | reaction mechanism, overview. The transformation from the initial O-coordination of substrate to the final N-coordination of product is achieved by electron transfer from T1 copper to T2 copper, rather than by the previously reported side-on coordination of a NO intermediate, which only takes place in the reduced enzyme. Role of structural change in the critical residue Asp98, which affects the energetics of substrate attachment and product release at the T2 copper reaction center, while it does not significantly affect the activation energy and reaction pathways of the nitrite reduction process | Achromobacter cycloclastes |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
nitrite + ferrocytochrome c + 2 H+ | - |
Achromobacter cycloclastes | nitric oxide + H2O + ferricytochrome c | - |
? |
Subunits | Comment | Organism |
---|---|---|
homotrimer | CuNiRs are organized as homotrimers with three identical monomers tightly associated together | Achromobacter cycloclastes |
Synonyms | Comment | Organism |
---|---|---|
copper-containing nitrite reductase | - |
Achromobacter cycloclastes |
CuNIR | - |
Achromobacter cycloclastes |
dissimilatory nitrite reductase | - |
Achromobacter cycloclastes |
NiR | - |
Achromobacter cycloclastes |
NirK | - |
Achromobacter cycloclastes |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
cytochrome c | - |
Achromobacter cycloclastes |
General Information | Comment | Organism |
---|---|---|
metabolism | the enzyme is involved in the denitrification anoxic process, which occurs in four reduction steps: initial conversion of nitrate to nitrite, followed by transformation of nitrite to nitric oxide, subsequent reduction of nitric oxide to nitrous oxide, and the final conversion of nitrous oxide to dinitrogen gas. All stages are catalyzed by complex metalloenzymes with different transition metal cofactors. Dissimilatory nitrite reductases (NiRs) catalyze the reduction of nitrite to nitric oxide, the committed step in denitrification. There are two main types: one containing iron (cd1NiRs) and the other copper (CuNiRs) | Achromobacter cycloclastes |
additional information | determination of the activation energies, transition states, and minimum energy pathways of CuNiR for reaction mechanism analysis. Structure modelling of the CuNiR active site involving residues His100, His135, His306, Asp98, His255, Ile257 and four water molecules. Structure-function analysis, detailed overview | Achromobacter cycloclastes |