Download MendeleyA three-domain copper-nitrite reductase with a unique sensing loop.
Opperman, D.J., Murgida, D.H., Dalosto, S.D., Brondino, C.D., Ferroni, F.M.(2019) IUCrJ 6: 248-258
- PubMed: 30867922
- DOI: https://doi.org/10.1107/S2052252519000241
- Primary Citation of Related Structures:
6HBE - PubMed Abstract:
Dissimilatory nitrite reductases are key enzymes in the denitrification pathway, reducing nitrite and leading to the production of gaseous products (NO, N 2 O and N 2 ). The reaction is catalysed either by a Cu-containing nitrite reductase (NirK) or by a cytochrome cd 1 nitrite reductase (NirS), as the simultaneous presence of the two enzymes has never been detected in the same microorganism. The thermophilic bacterium Thermus scotoductus SA-01 is an exception to this rule, harbouring both genes within a denitrification cluster, which encodes for an atypical NirK. The crystal structure of Ts NirK has been determined at 1.63 Å resolution. Ts NirK is a homotrimer with subunits of 451 residues that contain three copper atoms each. The N-terminal region possesses a type 2 Cu (T2Cu) and a type 1 Cu (T1Cu N ) while the C-terminus contains an extra type 1 Cu (T1Cu C ) bound within a cupredoxin motif. T1Cu N shows an unusual Cu atom coordination (His 2 -Cys-Gln) compared with T1Cu observed in NirKs reported so far (His 2 -Cys-Met). T1Cu C is buried at ∼5 Å from the molecular surface and located ∼14.1 Å away from T1Cu N ; T1Cu N and T2Cu are ∼12.6 Å apart. All these distances are compatible with an electron-transfer process T1Cu C → T1Cu N → T2Cu. T1Cu N and T2Cu are connected by a typical Cys-His bridge and an unexpected sensing loop which harbours a Ser CAT residue close to T2Cu, suggesting an alternative nitrite-reduction mechanism in these enzymes. Biophysicochemical and functional features of Ts NirK are discussed on the basis of X-ray crystallography, electron paramagnetic resonance, resonance Raman and kinetic experiments.
Organizational Affiliation:
Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, Free State 9300, South Africa.
