1dxc
From Proteopedia
(New page: 200px<br /><applet load="1dxc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dxc, resolution 1.4Å" /> '''CO COMPLEX OF MYOGLOB...) |
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| - | [[Image:1dxc.gif|left|200px]]<br /><applet load="1dxc" size=" | + | [[Image:1dxc.gif|left|200px]]<br /><applet load="1dxc" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1dxc, resolution 1.4Å" /> | caption="1dxc, resolution 1.4Å" /> | ||
'''CO COMPLEX OF MYOGLOBIN MB-YQR AT 100K'''<br /> | '''CO COMPLEX OF MYOGLOBIN MB-YQR AT 100K'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We determined the structure of the photolytic intermediate of a sperm | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1DXC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon] with SO4, HEM and CMO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1DXC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=HEM:'>HEM</scene> and <scene name='pdbligand=CMO:'>CMO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DXC OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Cutruzzola, F.]] | [[Category: Cutruzzola, F.]] | ||
[[Category: Schlichting, I.]] | [[Category: Schlichting, I.]] | ||
| - | [[Category: Sweet, R | + | [[Category: Sweet, R M.]] |
[[Category: Travaglini-Allocatelli, C.]] | [[Category: Travaglini-Allocatelli, C.]] | ||
[[Category: Vallone, B.]] | [[Category: Vallone, B.]] | ||
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[[Category: respiratory protein]] | [[Category: respiratory protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:21:30 2008'' |
Revision as of 10:21, 21 February 2008
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CO COMPLEX OF MYOGLOBIN MB-YQR AT 100K
Overview
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.
About this Structure
1DXC is a Single protein structure of sequence from Physeter catodon with , and as ligands. Full crystallographic information is available from OCA.
Reference
The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin., Brunori M, Vallone B, Cutruzzola F, Travaglini-Allocatelli C, Berendzen J, Chu K, Sweet RM, Schlichting I, Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2058-63. PMID:10681426
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