PDBsum entry 2ji3

Oxidoreductase

PDB id: 2ji3

Contents

Protein chains

126 a.a. *

Ligands

NO3

PER ×3

Metals

_FE ×8

_CA ×4

Waters ×309

* Residue conservation analysis

PDB id:

2ji3

Name:

Oxidoreductase

Title:

X-ray structure of the iron-peroxide intermediate of superoxide reductase (e114a mutant) from desulfoarculus baarsii

Structure:

Desulfoferrodoxin. Chain: a, b, c, d. Synonym: dfx,superoxide reductase,sor. Engineered: yes. Mutation: yes

Source:

Desulfarculus baarsii. Organism_taxid: 453230. Gene: dfx, rbo, deba_2050. Expressed in: escherichia coli dh5[alpha]. Expression_system_taxid: 668369.

Resolution:

1.95Å R-factor: 0.217 R-free: 0.249

Authors:

G.Katona,P.Carpentier,V.Niviere,P.Amara,V.Adam,J.Ohana,N.Tsanov, D.Bourgeois

Key ref:

G.Katona et al. (2007). Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme. Science, 316, 449-453. PubMed id: 17446401 DOI: 10.1126/science.1138885

Date:

24-Feb-07 Release date: 01-May-07

Protein chains

Q46495  (DFX_DESB2) -  Desulfoferrodoxin from Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802 / 2st14)

Seq: 126 a.a.

Struc: 126 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.15.1.2 - superoxide reductase.
• Reaction: reduced [rubredoxin] + superoxide + 2 H⁺ = oxidized [rubredoxin] + H2O2

reduced [rubredoxin] + superoxide + 2 × H(+) = oxidized [rubredoxin] (Bound ligand (Het Group name = PER) corresponds exactly) + H2O2

• Cofactor: Fe cation

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

Key reference

DOI no: 10.1126/science.1138885

Science 316:449-453 (2007)

PubMed id: 17446401

Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.

G.Katona, P.Carpentier, V.Nivière, P.Amara, V.Adam, J.Ohana, N.Tsanov, D.Bourgeois.

ABSTRACT

Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.

Selected figure(s)

Figure 1.
Fig. 1. Structural overview of SOR. The x-ray structure of the SOR-E114A homodimer in the native reduced state is shown as magenta (monomer A) and cyan (monomer B) ribbons with the exception of the LID loop (residues 45 to 49), which is colored in dark green and orange for monomers A and B, respectively. Reduced and oxidized iron atoms are shown as green and orange balls, respectively. (Inset) The active site of monomer B upon addition of H[2]O[2]. The residues coordinating the active iron (His^49, His^69, His^75, His^119, and Cys^116) as well as Lys^48 are represented as sticks. The bound peroxide ligand is shown as a red stick. Water molecules are shown as red balls. In order to support the diatomic nature of the peroxide intermediate, simulated annealed F[obs] – F[calc] maps omitting the distal or proximal oxygens of the O-O moiety, respectively, were calculated. The two maps are displayed in green (distal) and orange (proximal) at a contour level of 3.0 .

Figure 3.
Fig. 3. Raman spectra of SOR crystals. After reaction with H[2]O[2], the E114A SOR mutant reveals bands at 567 cm^–1 and 838 cm^–1, which are isotopically shifted to 563 cm^–1 and 802 cm^–1 in the presence of H ^18[2]O[2] (vertical gray lines). Similar Raman bands and ^18O isotopic shifts are observed in solution experiments (fig. S2). E114A-SOR in the native reduced form does not exhibit these bands; neither do crystals oxidized by hexachloroiridate(IV). The peaks at 567 cm^–1 and 838 cm^–1 are not substantially affected by exposure to an x-ray dose of 3 x 10^5 Gy, which is about the same dose as used for data collection.

The above figures are reprinted by permission from the AAAs: Science (2007, 316, 449-453) copyright 2007.

Figures were selected by the author.