PDBsum entry 1oq7

Oxidoreductase

PDB id: 1oq7

Contents

Protein chains

(+ 0 more) 346 a.a. *

Metals

_SR ×12

* Residue conservation analysis

PDB id:

1oq7

Name:

Oxidoreductase

Title:

The crystal structure of the iron free (apo-)form of stearoyl acyl carrier protein desaturase from ricinus communis (castor bean).

Structure:

Acyl-[acyl-carrier protein] desaturase. Chain: a, b, c, d, e, f. Synonym: stearoyl acyl carrier protein desaturase. Engineered: yes

Source:

Ricinus communis. Castor bean. Organism_taxid: 3988. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

3.20Å R-factor: 0.229 R-free: 0.257

Authors:

M.Moche,J.Shanklin,A.K.Ghoshal,Y.Lindqvist

Key ref:

M.Moche et al. (2003). Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates. J Biol Chem, 278, 25072-25080. PubMed id: 12704186 DOI: 10.1074/jbc.M301662200

Date:

07-Mar-03 Release date: 13-May-03

Protein chains

P22337  (STAD_RICCO) -  Stearoyl-[acyl-carrier-protein] 9-desaturase, chloroplastic from Ricinus communis

Seq: 396 a.a.

Struc: 346 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.19.2 - stearoyl-[acyl-carrier-protein] 9-desaturase.
• Reaction: octadecanoyl-[ACP] + 2 reduced [2Fe-2S]-[ferredoxin] + O2 + 2 H⁺ = (9Z)-octadecenoyl-[ACP] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 H2O

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

Key reference

DOI no: 10.1074/jbc.M301662200

J Biol Chem 278:25072-25080 (2003)

PubMed id: 12704186

Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates.

M.Moche, J.Shanklin, A.Ghoshal, Y.Lindqvist.

ABSTRACT

Delta9 stearoyl-acyl carrier protein (ACP) desaturase is a mu-oxo-bridged di-iron enzyme, which belongs to the structural class I of large helix bundle proteins and that catalyzes the NADPH and O2-dependent formation of a cis-double bond in stearoyl-ACP. The crystal structures of complexes with azide and acetate, respectively, as well as the apoand single-iron forms of Delta9 stearoyl-ACP desaturase from Ricinus communis have been determined. In the azide complex, the ligand forms a mu-1,3-bridge between the two iron ions in the active site, replacing a loosely bound water molecule. The structure of the acetate complex is similar, with acetate bridging the di-iron center in the same orientation with respect to the di-iron center. However, in this complex, the iron ligand Glu196 has changed its coordination mode from bidentate to monodentate, the first crystallographic observation of a carboxylate shift in Delta9 stearoyl-ACP desaturase. The two complexes are proposed to mimic a mu-1,2 peroxo intermediate present during catalytic turnover. There are striking structural similarities between the di-iron center in the Delta9 stearoyl-ACP desaturase-azide complex and in the reduced rubrerythrin-azide complex. This suggests that Delta9 stearoyl-ACP desaturase might catalyze the formation of water from exogenous hydrogen peroxide at a low rate. From the similarity in iron center structure, we propose that the mu-oxo-bridge in oxidized desaturase is bound to the di-iron center as in rubrerythrin and not as reported for the R2 subunit of ribonucleotide reductase and the hydroxylase subunit of methane monooxygenase. The crystal structure of the one-iron depleted desaturase species demonstrates that the affinities for the two iron ions comprising the di-iron center are not equivalent, Fe1 being the higher affinity site and Fe2 being the lower affinity site.

Selected figure(s)

Figure 6.
FIG. 6. Stereoview (a) and 2 F[o] - F[c] electron density map contoured at 1 (b) of the apo form of the desaturase di-iron center at 3.2-Å resolution. The absence of iron ions introduces flexibility in the coordinating residues of the original di-iron center.

Figure 8.
FIG. 8. Comparison of acetate complexes of desaturase (A) and methane monooxygenase hydroxylase (1MMO) (B). Hydrogen bonds to iron ligands are indicated with dotted lines. Glu142 and Asp228 in desaturase, corresponding to Asp143 and Asp242 in MMOH, make hydrogen bonds to the histidine iron ligands.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 25072-25080) copyright 2003.

Figures were selected by an automated process.