PDBsum entry 2dv6

Oxidoreductase

PDB id: 2dv6

Contents

Protein chains

(+ 0 more) 422 a.a. *

Metals

__K ×6

_CU ×18

Waters ×1803

* Residue conservation analysis

PDB id:

2dv6

Name:

Oxidoreductase

Title:

Crystal structure of nitrite reductase from hyphomicrobium denitrificans

Structure:

Nitrite reductase. Chain: a, b, c, d, e, f. Ec: 1.7.2.1

Source:

Hyphomicrobium denitrificans. Organism_taxid: 53399. Strain: a3151

Resolution:

2.20Å R-factor: 0.152 R-free: 0.165

Authors:

M.Nojiri,Y.Xie,T.Yamamoto,T.Inoue,S.Suzuki,Y.Kai

Key ref:

M.Nojiri et al. (2007). Structure and function of a hexameric copper-containing nitrite reductase. Proc Natl Acad Sci U S A, 104, 4315-4320. PubMed id: 17360521 DOI: 10.1073/pnas.0609195104

Date:

28-Jul-06 Release date: 20-Feb-07

Protein chains

Q8KKH4  (Q8KKH4_9HYPH) -  Copper-containing nitrite reductase from Hyphomicrobium denitrificans

Seq: 486 a.a.

Struc: 422 a.a.

Enzyme reactions

• Enzyme class: E.C.1.7.2.1 - nitrite reductase (NO-forming).
• Reaction: nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] + nitrite + 2 H⁺
• Cofactor: Cu cation or Fe cation; FAD

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0609195104

Proc Natl Acad Sci U S A 104:4315-4320 (2007)

PubMed id: 17360521

Structure and function of a hexameric copper-containing nitrite reductase.

M.Nojiri, Y.Xie, T.Inoue, T.Yamamoto, H.Matsumura, K.Kataoka, Deligeer, K.Yamaguchi, Y.Kai, S.Suzuki.

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.

Selected figure(s)

Figure 2.
Fig. 2. Cu centers in HdNIR. (a) Arrangement of the type 1 Cu[N], type 1 Cu[C], and type 2 Cu in the HdNIR molecule shown in the same orientation as in Fig. 1a. Blue, green, and gray spheres represent the type 1 Cu[N], type 1 Cu[C], and type 2 Cu, respectively. The figure was created by using PyMOL. (b and c Left) 2F[o] – F[c] difference maps for the Cu sites contoured at the 1.0 (light blue) and 6.5 levels (dark blue). (Right) Ball-and-stick representation of the same sites. The His-416 residue comes from the adjacent cupredoxin domain III. The figures were created by using TURBO-FRODO (www.afmb.univ-mrs.fr/-TURBO). Wat, Water molecule.

Figure 6.
Fig. 6. The molecular surface accessible for an electron donor protein. (a) The negatively and positively charged surfaces are shown in red and blue, respectively. (b) The blue, green, and gray spheres represent the type 1 Cu[N], type 1 Cu[C], and type 2 Cu, respectively. The Gln-76 and Glu-172 residues are located on the molecular surfaces of the N-terminal and C-terminal regions, respectively, which belong in the different monomers. The figure was created by using PyMOL. Surface electrostatic potential was calculated by using PyMOL APBS (http://apbs.sourceforge.net) tools.

Figures were selected by an automated process.