2R4Y

Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: H69V/I114M unliganded

Summary for 2R4Y

• Entry DOI: 10.2210/pdb2r4y/pdb
• Related: 2GRH 2R4W 2R4X 2R4Z 2Z85 2Z8A 3SDH 4SDH
• Descriptor: Globin-1, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: allostery, oxygen binding, oxygen affinity, cooperative hemoglobin, oxygen storage/transport, cytoplasm, heme, iron, metal-binding, oxygen transport
• Biological source: Scapharca inaequivalvis (ark clam)
• Cellular location: Cytoplasm: P02213
• Total number of polymer chains: 2
• Total formula weight: 33125.62

Authors

Knapp, J.E.,Royer Jr., W.E.,Nienhaus, K.,Palladino, P.,Nienhaus, G.U. (deposition date: 2007-09-02, release date: 2007-11-27, Last modification date: 2023-10-25)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2 Å)