Structure and function of a hexameric copper-containing nitrite reductase.
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.
Nojiri
Masaki
M
Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
Xie
Yong
Y
Inoue
Tsuyoshi
T
Yamamoto
Takahiko
T
Matsumura
Hiroyoshi
H
Kataoka
Kunishige
K
Deligeer
Yamaguchi
Kazuya
K
Kai
Yasushi
Y
Suzuki
Shinnichiro
S
D003300:Copper / Q000737:chemistry; D018360:Crystallography, X-Ray; D004583:Electrons; D020582:Hyphomicrobium / Q000201:enzymology*; D007700:Kinetics; D008958:Models, Molecular; D009569:Nitric Oxide / Q000737:chemistry; D009572:Nitrite Reductases / Q000737:chemistry* / Q000502:physiology*; D010084:Oxidation-Reduction; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D013997:Time Factors
D009569:Nitric Oxide; D003300:Copper; D009572:Nitrite Reductases; C052695:nitrite reductase, copper-containing