1J2C

Crystal structure of rat heme oxygenase-1 in complex with biliverdin IXalpha-iron cluster

1J2C の概要

• エントリーDOI: 10.2210/pdb1j2c/pdb
• 分子名称: Heme Oxygenase-1, FE (III) ION, BILIVERDINE IX ALPHA, ... (4 entities in total)
• 機能のキーワード: enzyme-product complex, bent helix, oxidoreductase
• 由来する生物種: Rattus norvegicus (Norway rat)
• 細胞内の位置: Microsome: P06762
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 31250.99

構造登録者

Sugishima, M.,Sakamoto, H.,Noguchi, M.,Fukuyama, K. (登録日: 2002-12-29, 公開日: 2003-09-02, 最終更新日: 2023-10-25)

主引用文献

Sugishima, M.,Sakamoto, H.,Higashimoto, Y.,Noguchi, M.,Fukuyama, K.
Crystal Structure of Rat Heme Oxygenase-1 in Complex with Biliverdin-Iron Chelate: CONFORMATIONAL CHANGE OF THE DISTAL HELIX DURING THE HEME CLEAVAGE REACTION.
J.Biol.Chem., 278:32352-32358, 2003

PubMed Abstract: The crystal structure of rat heme oxygenase-1 in complex with biliverdin-iron chelate (biliverdin(Fe)-HO-1), the immediate precursor of the final product, biliverdin, has been determined at a 2.4-A resolution. The electron density in the heme pocket clearly showed that the tetrapyrrole ring of heme is cleaved at the alpha-meso edge. Like the heme bound to HO-1, biliverdin-iron chelate is located between the distal and proximal helices, but its accommodation state seems to be less stable in light of the disordering of the solvent-exposed propionate and vinyl groups. The middle of the distal helix is shifted away from the center of the active site in biliverdin(Fe)-HO-1, increasing the size of the heme pocket. The hydrogen-bonding interaction between Glu-29 and Gln-38, considered to restrain the orientation of the proximal helix in the heme-HO-1 complex, was lost in biliverdin(Fe)-HO-1, leading to relaxation of the helix. Biliverdin has a distorted helical conformation; the lactam oxygen atom of its pyrrole ring-A interacted with Asp-140 through a hydrogen-bonding solvent network. Because of the absence of a distal water ligand, the iron atom is five-coordinated with His-25 and four pyrrole nitrogen atoms. The coordination geometry deviates considerably from a square pyramid, suggesting that the iron may be readily dissociated. We speculate that the opened conformation of the heme pocket facilitates sequential product release, first iron then biliverdin, and that because of biliverdin's increased flexibility, iron release triggers its slow dissociation.

PubMed: 12794075
DOI: 10.1074/jbc.M303682200

実験手法

X-RAY DIFFRACTION (2.4 Å)