NirK

nirK is the gene that encodes a copper-containing nitrite reductase (NirK), an enzyme that catalyzes the six-electron reduction of nitrite (NO2−) to nitric oxide (NO) in many bacterial denitrification pathways. Denitrification is a respiratory process used by some bacteria to gain energy under low-oxygen conditions, ultimately converting nitrate to dinitrogen gas.

The NirK enzyme is typically a periplasmic protein in Gram-negative bacteria and is often a homodimer, with each monomer containing two copper centers: a type 1 (electron transfer) center and a type 2 (catalytic) center. Electrons enter NirK from periplasmic electron carriers such as redox proteins and are transferred to the type 2 copper site, where nitrite is reduced to NO. NirK differs from the alternative nitrite reductase NirS, which is a cytochrome cd1 enzyme that uses a heme-based cofactor rather than copper.

Genetically, nirK is part of denitrification gene clusters found in a variety of soil, aquatic, and host-associated bacteria. Expression of nirK is typically induced under anaerobic or microaerophilic conditions when nitrite accumulates, and it is coordinated with other denitrification genes (nar, nor, nos) in response to oxygen and nitrogen oxide availability. nirK distribution and diversity have made it a common molecular marker for studying denitrifying communities via PCR-based surveys and metagenomics.

Ecological and evolutionary considerations include the presence of nirK in many, but not all, denitrifying bacteria, and its functional replacement by nirS in some lineages. The two enzymes perform the same overall reaction—nitrite reduction to NO—yet differ in their metal cofactors and structural families, reflecting distinct evolutionary solutions to ammonia and nitrate metabolism in prokaryotes.