3ECL

Carbonmonoxy Sperm Whale Myoglobin at 40 K: Laser on

3ECL の概要

• エントリーDOI: 10.2210/pdb3ecl/pdb
• 関連するPDBエントリー: 3E4N
• 分子名称: Myoglobin, PROTOPORPHYRIN IX CONTAINING FE, CARBON MONOXIDE, ... (5 entities in total)
• 機能のキーワード: haem protein, myoglobin, ligand migration, photodissociation, heme, iron, metal-binding, muscle protein, oxygen transport, transport
• 由来する生物種: Physeter catodon (Sperm whale)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 18071.57

構造登録者

Tomita, A.,Sato, T.,Ichiyanagi, K.,Nozawa, S.,Ichikawa, H.,Chollet, M.,Kawai, F.,Park, S.-Y.,Koshihara, S.,Adachi, S. (登録日: 2008-09-01, 公開日: 2009-02-24, 最終更新日: 2023-11-01)

主引用文献

Tomita, A.,Sato, T.,Ichiyanagi, K.,Nozawa, S.,Ichikawa, H.,Chollet, M.,Kawai, F.,Park, S.-Y.,Tsuduki, T.,Yamato, T.,Koshihara, S.,Adachi, S.
Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin
Proc.Natl.Acad.Sci.USA, 106:2612-2616, 2009

PubMed Abstract: Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.

PubMed: 19204297
DOI: 10.1073/pnas.0807774106

実験手法

X-RAY DIFFRACTION (1.21 Å)