1OQ4

The Crystal Structure of the Complex between Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean) and Azide.

Summary for 1OQ4

• Entry DOI: 10.2210/pdb1oq4/pdb
• Related: 1AFR 1OQ7 1OQ9 1OQB
• Descriptor: Acyl-[acyl-carrier protein] desaturase, FE (III) ION, AZIDE ION, ... (4 entities in total)
• Functional Keywords: di-iron enzyme, four-helix bundle, fatty acid biosynthesis, electron transfer, oxidoreductase
• Biological source: Ricinus communis (castor bean)
• Cellular location: Plastid, chloroplast: P22337
• Total number of polymer chains: 6
• Total formula weight: 251142.13

Authors

Moche, M.,Ghoshal, A.K.,Shanklin, J.,Lindqvist, Y. (deposition date: 2003-03-07, release date: 2003-05-13, Last modification date: 2023-10-25)

Primary citation

Moche, M.,Shanklin, J.,Ghoshal, A.,Lindqvist, Y.
Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta 9 stearoyl-ACP desaturase- implications for oxygen activation and catalytic intermediates.
J.Biol.Chem., 278:25072-25080, 2003

PubMed 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.

PubMed: 12704186
DOI: 10.1074/jbc.M301662200

Experimental method

X-RAY DIFFRACTION (2.4 Å)