4ZK8

Copper-containing nitrite reductase from thermophilic bacterium Geobacillus thermodenitrificans (Re-refined)

Replaces:  3WKO

Summary for 4ZK8

• Entry DOI: 10.2210/pdb4zk8/pdb
• Descriptor: Nitrite reductase, COPPER (II) ION, CHLORIDE ION, ... (10 entities in total)
• Functional Keywords: copper, oxidoreductase, denitrification, electron transfer, nitrite
• Biological source: Geobacillus thermodenitrificans NG80-2
• Total number of polymer chains: 1
• Total formula weight: 37598.82

Authors

Fukuda, Y.,Inoue, T. (deposition date: 2015-04-30, release date: 2015-05-20, Last modification date: 2024-03-20)

Primary citation

Fukuda, Y.,Tse, K.M.,Lintuluoto, M.,Fukunishi, Y.,Mizohata, E.,Matsumura, H.,Takami, H.,Nojiri, M.,Inoue, T.
Structural insights into the function of a thermostable copper-containing nitrite reductase
J.Biochem., 155:123-135, 2014

PubMed Abstract: Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO(-)2) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride- and formate-bound forms of wild type at 1.15 Å resolution and the nitrite-bound form of the C135A mutant at 1.90 Å resolution. The structure of C135A with nitrite displays a unique η(1)-O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wild-type CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CH-O hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the η(1)-O coordination manner is proposed.

PubMed: 24293549
DOI: 10.1093/jb/mvt107

Experimental method

X-RAY DIFFRACTION (1.15 Å)