2GRF

Crystal structure of Scapharca inaequivalvis HBI, M37V mutant in the absence of ligand

Summary for 2GRF

• Entry DOI: 10.2210/pdb2grf/pdb
• Related: 2GRH 2GRZ 4SDH
• Descriptor: Globin-1, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: invertebrate, hemoglobin, allostery, cooperativity, oxygen-binding, oxygen-transport, heme protein, oxygen storage-transport complex, oxygen storage/transport
• Biological source: Scapharca inaequivalvis (ark clam)
• Cellular location: Cytoplasm: P02213
• Total number of polymer chains: 2
• Total formula weight: 33103.45

Authors

Knapp, J.E.,Pahl, R.,Srajer, V.,Royer Jr., W.E. (deposition date: 2006-04-24, release date: 2006-05-09, Last modification date: 2023-08-30)

Primary citation

Knapp, J.E.,Pahl, R.,Srajer, V.,Royer Jr., W.E.
Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin.
Proc.Natl.Acad.Sci.Usa, 103:7649-7654, 2006

PubMed Abstract: Protein allostery provides mechanisms for regulation of biological function at the molecular level. We present here an investigation of global, ligand-induced allosteric transition in a protein by time-resolved x-ray diffraction. The study provides a view of structural changes in single crystals of Scapharca dimeric hemoglobin as they proceed in real time, from 5 ns to 80 micros after ligand photodissociation. A tertiary intermediate structure forms rapidly (<5 ns) as the protein responds to the presence of an unliganded heme within each R-state protein subunit, with key structural changes observed in the heme groups, neighboring residues, and interface water molecules. This intermediate lays a foundation for the concerted tertiary and quaternary structural changes that occur on a microsecond time scale and are associated with the transition to a low-affinity T-state structure. Reversal of these changes shows a considerable lag as a T-like structure persists well after ligand rebinding, suggesting a slow T-to-R transition.

PubMed: 16684887
DOI: 10.1073/pnas.0509411103

Experimental method

X-RAY DIFFRACTION (2.1 Å)