1J9Q

Crystal structure of nitrite soaked oxidized D98N AFNIR

Summary for 1J9Q

• Entry DOI: 10.2210/pdb1j9q/pdb
• Related: 1J9R 1J9S 1J9T
• Descriptor: COPPER-CONTAINING NITRITE REDUCTASE, COPPER (II) ION, NITRITE ION, ... (4 entities in total)
• Functional Keywords: cupredoxin fold copper nitrite, oxidoreductase
• Biological source: Alcaligenes faecalis
• Cellular location: Periplasm: P38501
• Total number of polymer chains: 3
• Total formula weight: 111152.28

Authors

Boulanger, M.J.,Murphy, M.E. (deposition date: 2001-05-28, release date: 2001-06-06, Last modification date: 2024-02-07)

Primary citation

Boulanger, M.J.,Murphy, M.E.
Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate
Biochemistry, 40:9132-9141, 2001

PubMed Abstract: High-resolution nitrite soaked oxidized and reduced crystal structures of two active site mutants, D98N and H255N, of nitrite reductase (NIR) from Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution. In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to the type II copper via its oxygen atoms in an asymmetric bidentate manner; however, elevated B-factors and weak electron density indicate that both nitrite and Asn98 are less ordered than in the native enzyme. This disorder likely results from the inability of the N delta 2 atom of Asn98 to form a hydrogen bond with the bound protonated nitrite, indicating that the hydrogen bond between Asp98 and nitrite in the native NIR structure is essential in anchoring nitrite in the active site for catalysis. In the oxidized nitrite soaked H255N crystal structure, nitrite does not displace the ligand water and is instead coordinated in an alternative mode via a single oxygen to the type II copper. His255 is clearly essential in defining the nitrite binding site despite the lack of direct interaction with the substrate in the native enzyme. The resulting pentacoordinate copper site in the H255N structure also serves as a model for a proposed transient intermediate in the catalytic mechanism consisting of a hydroxyl and nitric oxide molecule coordinated to the copper. The formation of an unusual dinuclear type I copper site in the reduced nitrite soaked D98N and H255N crystal structures may represent an evolutionary link between the mononuclear type I copper centers and dinuclear Cu(A) sites.

PubMed: 11478880
DOI: 10.1021/bi0107400

Experimental method

X-RAY DIFFRACTION (1.65 Å)