2R4Z

Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO

2R4Z の概要

• エントリーDOI: 10.2210/pdb2r4z/pdb
• 関連するPDBエントリー: 2GRH 2R4W 2R4X 2R4Y 2Z85 2Z8A 3SDH 4SDH
• 分子名称: Globin-1, PHOSPHATE ION, PROTOPORPHYRIN IX CONTAINING FE, ... (5 entities in total)
• 機能のキーワード: oxygen transport, allostery, oxygen affinity, oxygen storage/transport, cytoplasm, heme, iron, metal-binding, oxygen binding
• 由来する生物種: Scapharca inaequivalvis (ark clam)
• 細胞内の位置: Cytoplasm: P02213
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 33464.68

構造登録者

Knapp, J.E.,Royer Jr., W.E.,Nienhaus, K.,Palladino, P.,Nienhaus, G.U. (登録日: 2007-09-02, 公開日: 2007-11-27, 最終更新日: 2023-10-25)

主引用文献

Nienhaus, K.,Knapp, J.E.,Palladino, P.,Royer Jr., W.E.,Nienhaus, G.U.
Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca inaequivalvis
Biochemistry, 46:14018-14031, 2007

PubMed Abstract: Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.

PubMed: 18001141
DOI: 10.1021/bi7016798

実験手法

X-RAY DIFFRACTION (1.6 Å)