1DXC

CO complex of Myoglobin Mb-YQR at 100K

Summary for 1DXC

• Entry DOI: 10.2210/pdb1dxc/pdb
• Related: 1DXD
• Descriptor: MYOGLOBIN, PROTOPORPHYRIN IX CONTAINING FE, CARBON MONOXIDE, ... (5 entities in total)
• Functional Keywords: oxygen storage, co complex, respiratory protein
• Biological source: PHYSETER CATODON (SPERM WHALE)
• Total number of polymer chains: 1
• Total formula weight: 18393.94

Authors

Brunori, M.,Vallone, B.,Cutruzzola, F.,Travaglini-Allocatelli, C.,Berendzen, J.,Chu, K.,Sweet, R.M.,Schlichting, I. (deposition date: 2000-01-03, release date: 2000-04-02, Last modification date: 2024-05-08)

Primary citation

Brunori, M.,Vallone, B.,Cutruzzola, F.,Travaglini-Allocatelli, C.,Berendzen, J.,Chu, K.,Sweet, R.M.,Schlichting, I.
The Role of Cavities in Protein Dynamics: Crystal Structure of a Novel Photolytic Intermediate of Myoglobin
Proc.Natl.Acad.Sci.USA, 97:2058-, 2000

PubMed Abstract: We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-A resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe-CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 A from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F., Jr., Kuntz, I. D. & Petsko, G. A. (1984) Biochemistry 23, 2849-2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng et al. (1994) Nat. Struct. Biol. 1, 701-705] and room temperature [Srajer et al. (1996) Science 274, 1726-1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein.

PubMed: 10681426
DOI: 10.1073/PNAS.040459697

Experimental method

X-RAY DIFFRACTION (1.4 Å)