2ZT3: Carbonmonoxy Sperm Whale Myoglobin At 120 K: Laser On [750 Min]

Citation:
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.
PDB ID: 2ZT3Download
MMDB ID: 69808
PDB Deposition Date: 2008/9/18
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.21  Å
Source Organism:
Similar Structures:
Biological Unit for 2ZT3: monomeric; determined by author and by software (PISA)
Molecular Components in 2ZT3
Label Count Molecule
Protein (1 molecule)
1
Myoglobin
Molecule annotation
Chemicals (4 molecules)
1
1
2
1
3
2
* Click molecule labels to explore molecular sequence information.

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