4KVK

Crystal structure of Oryza sativa fatty acid alpha-dioxygenase

Summary for 4KVK

• Entry DOI: 10.2210/pdb4kvk/pdb
• Related: 4KVJ 4KVL
• Descriptor: Fatty acid alpha-oxidase, SODIUM ION, PROTOPORPHYRIN IX CONTAINING FE, ... (11 entities in total)
• Functional Keywords: piox, cox-like protein, fatty acid alpha-dioxygenase, heme binding, calcium binding, monotopic membrane protein, oxidoreductase
• Biological source: Oryza sativa (red rice)
• Total number of polymer chains: 1
• Total formula weight: 73690.13

Authors

Zhu, G.,Koszelak-Rosenblum, M.,Malkowski, M.G. (deposition date: 2013-05-22, release date: 2013-08-21, Last modification date: 2024-02-28)

Primary citation

Zhu, G.,Koszelak-Rosenblum, M.,Malkowski, M.G.
Crystal structures of alpha-dioxygenase from Oryza sativa: Insights into substrate binding and activation by hydrogen peroxide.
Protein Sci., 22:1432-1438, 2013

PubMed Abstract: α-Dioxygenases (α-DOX) are heme-containing enzymes found predominantly in plants and fungi, where they generate oxylipins in response to pathogen attack. α-DOX oxygenate a variety of 14-20 carbon fatty acids containing up to three unsaturated bonds through stereoselective removal of the pro-R hydrogen from the α-carbon by a tyrosyl radical generated via the oxidation of the heme moiety by hydrogen peroxide (H2 O2 ). We determined the X-ray crystal structures of wild type α-DOX from Oryza sativa, the wild type enzyme in complex with H2 O2 , and the catalytically inactive Y379F mutant in complex with the fatty acid palmitic acid (PA). PA binds within the active site cleft of α-DOX such that the carboxylate forms ionic interactions with His-311 and Arg-559. Thr-316 aids in the positioning of carbon-2 for hydrogen abstraction. Twenty-five of the twenty eight contacts made between PA and residues lining the active site occur within the carboxylate and first eight carbons, indicating that interactions within this region of the substrate are responsible for governing selectivity. Comparison of the wild type and H2 O2 structures provides insight into enzyme activation. The binding of H2 O2 at the distal face of the heme displaces residues His-157, Asp-158, and Trp-159 ≈ 2.5 Å from their positions in the wild type structure. As a result, the Oδ2 atom of Asp-158 interacts with the Ca atom in the calcium binding loop, the side chains of Trp-159 and Trp-213 reorient, and the guanidinium group of Arg-559 is repositioned near Tyr-379, poised to interact with the carboxylate group of the substrate.

PubMed: 23934749
DOI: 10.1002/pro.2327

Experimental method

X-RAY DIFFRACTION (1.98 Å)