5YTL

Crystal structure of Geobacillus thermodenitrificans copper-containing nitrite reductase determined with an anaerobically manipulated crystal

Summary for 5YTL

• Entry DOI: 10.2210/pdb5ytl/pdb
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, (4R)-2-METHYLPENTANE-2,4-DIOL, ... (6 entities in total)
• Functional Keywords: copper, nitrite reductase, oxidoreductase
• Biological source: Geobacillus thermodenitrificans
• Total number of polymer chains: 1
• Total formula weight: 36137.19

Authors

Fukuda, Y.,Matsusaki, T.,Tse, K.M.,Mizohata, E.,Murphy, M.E.P.,Inoue, T. (deposition date: 2017-11-19, release date: 2018-08-22, Last modification date: 2024-03-27)

Primary citation

Fukuda, Y.,Matsusaki, T.,Tse, K.M.,Mizohata, E.,Murphy, M.E.P.,Inoue, T.
Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.
Acta Crystallogr D Struct Biol, 74:769-777, 2018

PubMed Abstract: Copper-containing nitrite reductases (CuNIRs) are multifunctional enzymes that catalyse the one-electron reduction of nitrite (NO) to nitric oxide (NO) and the two-electron reduction of dioxygen (O) to hydrogen peroxide (HO). In contrast to the mechanism of nitrite reduction, that of dioxygen reduction is poorly understood. Here, results from anaerobic synchrotron-radiation crystallography (SRX) and aerobic in-house radiation crystallography (iHRX) with a CuNIR from the thermophile Geobacillus thermodenitrificans (GtNIR) support the hypothesis that the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper (T2Cu) site of GtNIR during SRX experiments. The anaerobic SRX structure showed a dual conformation of one water molecule as an axial ligand in the T2Cu site, while previous aerobic SRX GtNIR structures were refined as diatomic molecule-bound states. Moreover, an SRX structure of the C135A mutant of GtNIR with peroxide bound to the T2Cu atom was determined. The peroxide molecule was mainly observed in a side-on binding manner, with a possible minor end-on conformation. The structures provide insights into dioxygen chemistry in CuNIRs and hence help to unmask the other face of CuNIRs.

PubMed: 30082512
DOI: 10.1107/S2059798318010082

Experimental method

X-RAY DIFFRACTION (1.401 Å)