PDBsum entry 2dwt

Oxidoreductase

PDB id: 2dwt

Contents

Protein chain

329 a.a. *

Ligands

NO2 ×2

Metals

_CU ×2

Waters ×104

* Residue conservation analysis

PDB id:

2dwt

Name:

Oxidoreductase

Title:

Cu-containing nitrite reductase at ph 6.0 with bound nitrite

Structure:

Copper-containing nitrite reductase. Chain: a. Synonym: cu-nir. Engineered: yes

Source:

Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: 2.4.3. Gene: nirk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PDB file)

Resolution:

1.90Å R-factor: 0.199 R-free: 0.235

Authors:

F.Jacobson

Key ref:

F.Jacobson et al. (2007). pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase. J Biol Chem, 282, 6347-6355. PubMed id: 17148448 DOI: 10.1074/jbc.M605746200

Date:

17-Aug-06 Release date: 05-Dec-06

Protein chain

Q53239  (NIR_RHOS5) -  Copper-containing nitrite reductase from Cereibacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)

Seq: 374 a.a.

Struc: 329 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⁺

nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] + nitrite + 2 × H(+) (Bound ligand (Het Group name = NO2) corresponds exactly)

• Cofactor: Cu cation or Fe cation; FAD

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

reference

DOI no: 10.1074/jbc.M605746200

J Biol Chem 282:6347-6355 (2007)

PubMed id: 17148448

pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase.

F.Jacobson, A.Pistorius, D.Farkas, W.De Grip, O.Hansson, L.Sjölin, R.Neutze.

ABSTRACT

Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

Selected figure(s)

Figure 2.
FIGURE 2. Stereo view of nitrite bound to the type 2 copper ion in RsNiR. a, at pH 6.0 showing full occupancy and with 2F[o] - F[c] electron density contoured at level 1.0. b, at pH 8.4 with half-occupancy and with 2F[o] - F[c] electron density contoured at level 0.9. The flexibility of His-287 at pH 8.4 can be seen as a rotation of the imidazole ring (b).

Figure 3.
FIGURE 3. Stereo view illustrating the ligating solvent molecule that coordinates the oxidized type 2 copper ion in Cu-NiRs. a and b, pH6(a) and at pH 8.4 (b), both with 2F[o] - F[c] electron density contoured at level 1.0. Asp-129 forms an H-bond to the solvent ligand at pH 6.0 (a), but this bond is absent at pH 8.4 (b). The flexibility of His-287 at pH 8.4 can be seen as a movement of the imidazole ring toward the type 2 copper ion (b).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 6347-6355) copyright 2007.

Figures were selected by an automated process.