2DV6

Crystal structure of nitrite reductase from Hyphomicrobium denitrificans

Summary for 2DV6

• Entry DOI: 10.2210/pdb2dv6/pdb
• Descriptor: Nitrite reductase, COPPER (II) ION, POTASSIUM ION, ... (4 entities in total)
• Functional Keywords: nitrite, electron transfer, reduction, denitrification, oxidoreductase
• Biological source: Hyphomicrobium denitrificans
• Total number of polymer chains: 6
• Total formula weight: 290710.21

Authors

Nojiri, M.,Xie, Y.,Yamamoto, T.,Inoue, T.,Suzuki, S.,Kai, Y. (deposition date: 2006-07-28, release date: 2007-02-20, Last modification date: 2023-10-25)

Primary citation

Nojiri, M.,Xie, Y.,Inoue, T.,Yamamoto, T.,Matsumura, H.,Kataoka, K.,Deligeer,Yamaguchi, K.,Kai, Y.,Suzuki, S.
Structure and function of a hexameric copper-containing nitrite reductase.
Proc.Natl.Acad.Sci.USA, 104:4315-4320, 2007

PubMed Abstract: Dissimilatory nitrite reductase (NIR) is a key enzyme in denitrification, catalyzing the first step that leads to gaseous products (NO, N(2)O, and N(2)). We have determined the crystal structure of a Cu-containing NIR from a methylotrophic denitrifying bacterium, Hyphomicrobium denitrificans, at 2.2-A resolution. The overall structure of this H. denitrificans NIR reveals a trigonal prism-shaped molecule in which a monomer consisting of 447 residues and three Cu atoms is organized into a unique hexamer (i.e., a tightly associated dimer of trimers). Each monomer is composed of an N-terminal region containing a Greek key beta-barrel folding domain, cupredoxin domain I, and a C-terminal region containing cupredoxin domains II and III. Both cupredoxin domains I and II bind one type 1 Cu and are combined with a long loop comprising 31 amino acid residues. The type 2 Cu is ligated at the interface between domain II of one monomer and domain III of an adjacent monomer. Between the two trimeric C-terminal regions are three interfaces formed by an interaction between the domains I, and the type 1 Cu in the domain is required for dimerization of the trimer. The type 1 Cu in domain II functions as an electron acceptor from an electron donor protein and then transfers an electron to the type 2 Cu, binding the substrate to reduce nitrite to NO. The discussion of the intermolecular electron transfer process from cytochrome c(550) to the H. denitrificans NIR is based on x-ray crystallographic and kinetic results.

PubMed: 17360521
DOI: 10.1073/pnas.0609195104

Experimental method

X-RAY DIFFRACTION (2.2 Å)