1QYB

X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures

1QYB の概要

• エントリーDOI: 10.2210/pdb1qyb/pdb
• 関連するPDBエントリー: 1LKM
• 分子名称: Rubrerythrin, FE (III) ION, ZINC ION, ... (5 entities in total)
• 機能のキーワード: rubrerythrin, zinc-substituted, diiron four-helix bundle, rubredoxin-like, electron transport
• 由来する生物種: Desulfovibrio vulgaris subsp. 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: 21850.44

構造登録者

Jin, S.,Kurtz, D.M.,Liu, Z.J.,Rose, J.,Wang, B.C. (登録日: 2003-09-10, 公開日: 2004-03-30, 最終更新日: 2023-08-23)

主引用文献

Jin, S.,Kurtz, D.M.,Liu, Z.J.,Rose, J.,Wang, B.C.
X-ray Crystal Structure of Desulfovibrio vulgaris Rubrerythrin with Zinc Substituted into the [Fe(SCys)(4)] Site and Alternative Diiron Site Structures.
Biochemistry, 43:3204-3213, 2004

PubMed Abstract: The X-ray crystal structure of recombinant Desulfovibrio vulgaris rubrerythrin (Rbr) that was subjected to metal constitution first with zinc and then iron, yielding ZnS(4)Rbr, is reported. A [Zn(SCys)(4)] site with no iron and a diiron site with no appreciable zinc in ZnS(4)Rbr were confirmed by analysis of the anomalous scattering data. Partial reduction of the diiron site occurred during the synchrotron X-ray irradiation at 95 K, resulting in two different diiron site structures in the ZnS(4)Rbr crystal. These two structures can be classified as containing mixed-valent Fe1(III)(mu-OH(-))(mu-GluCO(2)(-))(2)Fe2(II) and Fe1(II)(mu-GluCO(2)(-))(2)Fe2(III)-OH(-) cores. The data do not show any evidence for alternative positions of the protein or solvent ligands. The iron and ligand positions of the solvent-bridged site are close to those of the diferric site in all-iron Rbr. The diiron site with only the two carboxylato bridges differs by an approximately 2 A shift in the position of Fe1, which changes from six- to four-coordination. The Fe1- - -Fe2 distance (3.6 A) in this latter site is significantly longer than that of the site with the additional solvent bridge (3.4 A) but significantly shorter than that previously reported for the diferrous site (4.0 A) in all-iron Rbr. The apparent redox-induced movement of Fe1 at 95 K in the ZnS(4)Rbr crystal implies an extremely low activation barrier, which is consistent with the rapid (approximately 30 s(-1)) room temperature turnover of the all-iron Rbr during its catalysis of two-electron reduction of hydrogen peroxide. ZnS(4)Rbr does not show peroxidase activity, presumably because the [Zn(SCys)(4)] site, unlike the [Fe(SCys)(4)] site, cannot mediate electron transfer to the diiron site. One or both of the diiron site structures in the cryoreduced ZnS(4)Rbr crystal are likely to represent that (those) of transient mixed-valent diiron site(s) that must occur upon return of the diferric to the diferrous oxidation level during peroxidase turnover.

PubMed: 15023070
DOI: 10.1021/bi0356193

実験手法

X-RAY DIFFRACTION (1.75 Å)