2PP8

Formate bound to oxidized wild type AfNiR

Summary for 2PP8

• Entry DOI: 10.2210/pdb2pp8/pdb
• Related: 1SJM 1SNR 2FJS
• Descriptor: Copper-containing nitrite reductase, COPPER (I) ION, COPPER (II) ION, ... (7 entities in total)
• Functional Keywords: nitrite reductase, denitrification, bacteria, oxidoreductase
• Biological source: Alcaligenes faecalis
• Cellular location: Periplasm: P38501
• Total number of polymer chains: 3
• Total formula weight: 111749.79

Authors

Tocheva, E.I.,Eltis, L.D.,Murphy, M.E.P. (deposition date: 2007-04-28, release date: 2008-04-01, Last modification date: 2024-02-21)

Primary citation

Tocheva, E.I.,Eltis, L.D.,Murphy, M.E.
Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules.
Biochemistry, 47:4452-4460, 2008

PubMed Abstract: The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.

PubMed: 18358002
DOI: 10.1021/bi7020537

Experimental method

X-RAY DIFFRACTION (1.5 Å)