Literature summary for 1.7.2.1 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 .

Crystallization (Commentary)

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

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

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/ Products (Substrates)

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

Organism	UniProt	Comment	Textmining
Geobacillus thermodenitrificans	A4IL26	-	-
Geobacillus thermodenitrificans NG80-2	A4IL26	-	-

Reaction

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	a

Substrates and Products (Substrate)

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

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

Cofactor

Cofactor	Comment	Organism	Structure
cytochrome c	-	Geobacillus thermodenitrificans

General Information

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