2PPD

Oxidized H145A mutant of AfNiR bound to nitric oxide

Summary for 2PPD

• Entry DOI: 10.2210/pdb2ppd/pdb
• Related: 1SNR
• Descriptor: Copper-containing nitrite reductase, COPPER (I) ION, COPPER (II) ION, ... (7 entities in total)
• Functional Keywords: h145a, nitrite reductase, nitric oxide, denitrification, bacteria, oxidoreductase
• Biological source: Alcaligenes faecalis
• Cellular location: Periplasm: P38501
• Total number of polymer chains: 3
• Total formula weight: 111612.93

Authors

Tocheva, E.I.,Murphy, M.E.P. (deposition date: 2007-04-28, release date: 2008-01-15, Last modification date: 2024-02-21)

Primary citation

Tocheva, E.I.,Rosell, F.I.,Mauk, A.G.,Murphy, M.E.
Stable copper-nitrosyl formation by nitrite reductase in either oxidation state
Biochemistry, 46:12366-12374, 2007

PubMed Abstract: Nitrite reductase (NiR) is an enzyme that uses type 1 and type 2 copper sites to reduce nitrite to nitric oxide during bacterial denitrification. A copper-nitrosyl intermediate is a proposed, yet poorly characterized feature of the NiR catalytic cycle. This intermediate is formally described as Cu(I)-NO+ and is proposed to be formed at the type 2 copper site after nitrite binding and electron transfer from the type 1 copper site. In this study, copper-nitrosyl complexes were formed by prolonged exposure of exogenous NO to crystals of wild-type and two variant forms of NiR from Alcaligenes faecalis (AfNiR), and the structures were determined to 1.8 A or better resolution. Exposing oxidized wild-type crystals to NO results in the reverse reaction and formation of nitrite that remains bound at the active site. In a type 1 copper site mutant (H145A) that is incapable of electron transfer to the type 2 site, the reverse reaction is not observed. Instead, in both oxidized and reduced H145A crystals, NO is observed bound in a side-on manner to the type 2 copper. In AfNiR, Asp98 forms hydrogen bonds to both substrate and product bound to the type 2 Cu. In the D98N variant, NO is bound side-on but is more disordered when observed for the wild-type enzyme. The solution EPR spectra of the crystallographically characterized NiR-NO complexes indicate the presence of an oxidized type 2 copper site and thus are interpreted as resulting from stable copper-nitrosyls and formally assigned as Cu(II)-NO-. A reaction scheme in which a second NO molecule is oxidized to nitrite can account for the formation of a Cu(II)-NO- species after exposure of the oxidized H145A variant to NO gas.

PubMed: 17924665
DOI: 10.1021/bi701205j

Experimental method

X-RAY DIFFRACTION (1.8 Å)