6HBE

Cu-containing nitrite reductase (NirK) from Thermus scotoductus SA-01

Summary for 6HBE

• Entry DOI: 10.2210/pdb6hbe/pdb
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: nitrite reductase, three-domain nirk, denitrification, oxidoreductase
• Biological source: Thermus scotoductus (strain ATCC 700910 / SA-01)
• Total number of polymer chains: 3
• Total formula weight: 149788.12

Authors

Opperman, D.J.,Ferroni, F.M. (deposition date: 2018-08-10, release date: 2019-01-23, Last modification date: 2024-01-17)

Primary citation

Opperman, D.J.,Murgida, D.H.,Dalosto, S.D.,Brondino, C.D.,Ferroni, F.M.
A three-domain copper-nitrite reductase with a unique sensing loop.
Iucrj, 6:248-258, 2019

PubMed Abstract: Dissimilatory nitrite reductases are key enzymes in the denitrification pathway, reducing nitrite and leading to the production of gaseous products (NO, NO and N). The reaction is catalysed either by a Cu-containing nitrite reductase (NirK) or by a cytochrome nitrite reductase (NirS), as the simultaneous presence of the two enzymes has never been detected in the same microorganism. The thermophilic bacterium 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 NirK has been determined at 1.63 Å resolution. 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) while the C-terminus contains an extra type 1 Cu (T1Cu) bound within a cupredoxin motif. T1Cu shows an unusual Cu atom coordination (His-Cys-Gln) compared with T1Cu observed in NirKs reported so far (His-Cys-Met). T1Cu is buried at ∼5 Å from the molecular surface and located ∼14.1 Å away from T1Cu; T1Cu and T2Cu are ∼12.6 Å apart. All these distances are compatible with an electron-transfer process T1Cu → T1Cu → T2Cu. T1Cu and T2Cu are connected by a typical Cys-His bridge and an unexpected sensing loop which harbours a Ser residue close to T2Cu, suggesting an alternative nitrite-reduction mechanism in these enzymes. Biophysicochemical and functional features of NirK are discussed on the basis of X-ray crystallography, electron paramagnetic resonance, resonance Raman and kinetic experiments.

PubMed: 30867922
DOI: 10.1107/S2052252519000241

Experimental method

X-RAY DIFFRACTION (1.63 Å)