6hbe | pdb_00006hbe

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

spinqualitylabelsall models 6hbe, resolution 1.63Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6hbe is a 3 chain structure with sequence from Thess. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, CU Gene: TSC_c17620 (THESS) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Dissimilatory nitrite reductases are key enzymes in the denitrification pathway, reducing nitrite and leading to the production of gaseous products (NO, N2O and N2). 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 TsNirK has been determined at 1.63 A resolution. TsNirK 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 (T1CuN) while the C-terminus contains an extra type 1 Cu (T1CuC) bound within a cupredoxin motif. T1CuN shows an unusual Cu atom coordination (His2-Cys-Gln) compared with T1Cu observed in NirKs reported so far (His2-Cys-Met). T1CuC is buried at approximately 5 A from the molecular surface and located approximately 14.1 A away from T1CuN; T1CuN and T2Cu are approximately 12.6 A apart. All these distances are compatible with an electron-transfer process T1CuC --> T1CuN --> T2Cu. T1CuN and T2Cu are connected by a typical Cys-His bridge and an unexpected sensing loop which harbours a SerCAT residue close to T2Cu, suggesting an alternative nitrite-reduction mechanism in these enzymes. Biophysicochemical and functional features of TsNirK are discussed on the basis of X-ray crystallography, electron paramagnetic resonance, resonance Raman and kinetic experiments. A three-domain copper-nitrite reductase with a unique sensing loop.,Opperman DJ, Murgida DH, Dalosto SD, Brondino CD, Ferroni FM IUCrJ. 2019 Feb 9;6(Pt 2):248-258. doi: 10.1107/S2052252519000241. eCollection, 2019 Mar 1. PMID:30867922 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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