1LKO

Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form

1LKO の概要

• エントリーDOI: 10.2210/pdb1lko/pdb
• 関連するPDBエントリー: 1LKM 1LKP
• 分子名称: Rubrerythrin all-iron(II) form, FE (II) ION (3 entities in total)
• 機能のキーワード: rubrerythrin, reduced form, diiron, four-helix bundle, rubredoxin-like, electron transport
• 由来する生物種: Desulfovibrio vulgaris
• 細胞内の位置: Cytoplasm (Potential): P24931
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 21744.82

構造登録者

Jin, S.,Kurtz Jr., D.M.,Liu, Z.J.,Rose, J.,Wang, B.C. (登録日: 2002-04-25, 公開日: 2002-09-18, 最終更新日: 2024-02-14)

主引用文献

Jin, S.,Kurtz Jr., D.M.,Liu, Z.J.,Rose, J.,Wang, B.C.
X-ray Crystal Structures of Reduced Rubrerythrin and its Azide Adduct: A Structure-Based Mechanism for a Non-Heme DiIron Peroxidase
J.Am.Chem.Soc., 124:9845-9855, 2002

PubMed Abstract: Rubrerythrin (Rbr) is a 44-kDa homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like [Fe(SCys)(4)] site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. The diiron site structure resembles those found in O2-activating diiron enzymes. However, Rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). The diferrous site in all-ferrous Rbr (Rbr(red)) shows a much greater reactivity with H2O2 than does the diferric site in all-ferric Rbr (Rbr(ox)), but only the latter structure has been reported. Here we report the X-ray crystal structures of the recombinant Rbr(red) from the sulfate reducing bacterium, Desulfovibrio vulgaris, as well as its azide adduct (Rbr(red)N3). We have also redetermined the structure of Rbr(ox) to a higher resolution than previously reported. The structural differences between Rbr(ox) and Rbr(red) are localized entirely at the diiron site. The most striking structural change upon reduction of the diferric to the diferrous site of Rbr is a 1.8-A movement of one iron away from a unique glutamate carboxylate ligand and toward a trans-disposed histidine side chain, which replaces the glutamate as a ligand. This movement increases the inter-iron distance from 3.3 to 4 A. Rbr(red)N(3) shows this same iron movement and His-->Glu ligand replacement relative to Rbr(ox), and, in addition, an azide coordinated to the diiron site in a cis mu-1,3 fashion, replacing two solvent ligands in Rbr(red). Relative to those in O2-activating enzymes, the bridging carboxylate ligation of the Rbr diiron site is less flexible upon diferric/diferrous interconversion. The diferrous site is also much more rigid, symmetrical, and solvent-exposed than those in O2-activating enzymes. On the basis of these unique structural features, a mechanism is proposed for facile reduction of hydrogen peroxide by Rbr involving a cis mu-eta(2) H2O2 diferrous intermediate.

PubMed: 12175244
DOI: 10.1021/ja026587u

実験手法

X-RAY DIFFRACTION (1.63 Å)