Structure and function of a hexameric copper-containing nitrite reductase

• Masaki Nojiri

  *Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan;

• Yong Xie

  Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan;

• Tsuyoshi Inoue

  Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan;

• Takahiko Yamamoto

  Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan;

• Hiroyoshi Matsumura

  Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan;

• Kunishige Kataoka

  Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan; and

• Deligeer

  Department of Chemistry and Environmental Science, Inner Mongolia Normal University, Hohhot 010022, Inner Mongolia, People's Republic of China

• Kazuya Yamaguchi

  *Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan;

• Yasushi Kai

  Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan;

• Shinnichiro Suzuki

  *Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan;

抄録

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-Å 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 β-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.

収録刊行物

• Proceedings of the National Academy of Sciences

  Proceedings of the National Academy of Sciences 104 (11), 4315-4320, 2007-03-13

  Proceedings of the National Academy of Sciences

キーワード

• Multidisciplinary

詳細情報

• CRID: 1363388845391679872
• NII論文ID: 30026219792
• DOI: 10.1073/pnas.0609195104
• ISSN: 10916490
• ISSN: 00278424
• Web Site: https://pnas.org/doi/pdf/10.1073/pnas.0609195104
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