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Literature summary for 1.7.2.1 extracted from

  • Li, Y.; Hodak, M.; Bernholc, J.
    Enzymatic mechanism of copper-containing nitrite reductase (2015), Biochemistry, 54, 1233-1242 .
    View publication on PubMed

Metals/Ions

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/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
nitrite + ferrocytochrome c + 2 H+ Achromobacter cycloclastes
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nitric oxide + H2O + ferricytochrome c
-
?

Organism

Organism UniProt Comment Textmining
Achromobacter cycloclastes P25006
-
-

Reaction

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 and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
nitrite + ferrocytochrome c + 2 H+
-
Achromobacter cycloclastes nitric oxide + H2O + ferricytochrome c
-
?

Subunits

Subunits Comment Organism
homotrimer CuNiRs are organized as homotrimers with three identical monomers tightly associated together Achromobacter cycloclastes

Synonyms

Synonyms Comment Organism
copper-containing nitrite reductase
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Achromobacter cycloclastes
CuNIR
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Achromobacter cycloclastes
dissimilatory nitrite reductase
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Achromobacter cycloclastes
NiR
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Achromobacter cycloclastes
NirK
-
Achromobacter cycloclastes

Cofactor

Cofactor Comment Organism Structure
cytochrome c
-
Achromobacter cycloclastes

General Information

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